def make_write_jobs(mseqs, fasta_file, seqs_bed_file, seqs_cov_dir, tfr_dir,
gi, unmap_npy, targets_start, sum_targets, options):
"""Make basenji_data_write.py jobs for one genome."""
write_jobs = []
for tvt_set in ['train', 'valid', 'test']:
tvt_set_indexes = [
i for i in range(len(mseqs)) if mseqs[i].label == tvt_set
]
tvt_set_start = tvt_set_indexes[0]
tvt_set_end = tvt_set_indexes[-1] + 1
tfr_i = 0
tfr_start = tvt_set_start
tfr_end = min(tfr_start + options.seqs_per_tfr, tvt_set_end)
while tfr_start <= tvt_set_end:
tfr_stem = '%s/%s-%d-%d' % (tfr_dir, tvt_set, gi, tfr_i)
cmd = 'basenji_data_write.py'
cmd += ' -s %d' % tfr_start
cmd += ' -e %d' % tfr_end
cmd += ' -g %d' % gi
cmd += ' --ts %d' % targets_start
cmd += ' --te %d' % sum_targets
if unmap_npy is not None:
cmd += ' -u %s' % unmap_npy
if options.umap_set is not None:
cmd += ' --umap_set %f' % options.umap_set
cmd += ' %s' % fasta_file
cmd += ' %s' % seqs_bed_file
cmd += ' %s' % seqs_cov_dir
cmd += ' %s.tfr' % tfr_stem
if options.run_local:
cmd += ' &> %s.err' % tfr_stem
write_jobs.append(cmd)
else:
j = slurm.Job(cmd,
name='write_%s-%d' % (tvt_set, tfr_i),
out_file='%s.out' % tfr_stem,
err_file='%s.err' % tfr_stem,
queue='standard',
mem=15000,
time='12:0:0')
write_jobs.append(j)
# update
tfr_i += 1
tfr_start += options.seqs_per_tfr
tfr_end = min(tfr_start + options.seqs_per_tfr, tvt_set_end)
return write_jobs
def make_read_jobs(seqs_bed_file, targets_df, gi, seqs_cov_dir, options):
"""Make basenji_data_read.py jobs for one genome."""
# filter targets
targets_df_gi = targets_df[targets_df.genome == gi]
read_jobs = []
for ti in range(targets_df_gi.shape[0]):
genome_cov_file = targets_df_gi["file"].iloc[ti]
seqs_cov_stem = "%s/%d-%d" % (seqs_cov_dir, gi, ti)
seqs_cov_file = "%s.h5" % seqs_cov_stem
clip_ti = None
if "clip" in targets_df_gi.columns:
clip_ti = targets_df_gi["clip"].iloc[ti]
scale_ti = 1
if "scale" in targets_df_gi.columns:
scale_ti = targets_df_gi["scale"].iloc[ti]
if os.path.isfile(seqs_cov_file):
print("Skipping existing %s" % seqs_cov_file, file=sys.stderr)
else:
cmd = "basenji_data_read.py"
cmd += " -u %s" % targets_df_gi["sum_stat"].iloc[ti]
cmd += " -w %d" % options.pool_width
if clip_ti is not None:
cmd += " -c %f" % clip_ti
if options.soft_clip:
cmd += " --soft"
cmd += " -s %f" % scale_ti
if options.blacklist_beds[gi]:
cmd += " -b %s" % options.blacklist_beds[gi]
cmd += " %s" % genome_cov_file
cmd += " %s" % seqs_bed_file
cmd += " %s" % seqs_cov_file
if options.run_local:
cmd += " &> %s.err" % seqs_cov_stem
read_jobs.append(cmd)
else:
j = slurm.Job(
cmd,
name="read_t%d" % ti,
out_file="%s.out" % seqs_cov_stem,
err_file="%s.err" % seqs_cov_stem,
queue="standard",
mem=15000,
time="12:0:0",
)
read_jobs.append(j)
return read_jobs
def make_read_jobs(seqs_bed_file, targets_df, gi, seqs_cov_dir, options):
"""Make basenji_data_read.py jobs for one genome."""
# filter targets
targets_df_gi = targets_df[targets_df.genome == gi]
read_jobs = []
for ti in range(targets_df_gi.shape[0]):
genome_cov_file = targets_df_gi['file'].iloc[ti]
seqs_cov_stem = '%s/%d-%d' % (seqs_cov_dir, gi, ti)
seqs_cov_file = '%s.h5' % seqs_cov_stem
clip_ti = None
if 'clip' in targets_df_gi.columns:
clip_ti = targets_df_gi['clip'].iloc[ti]
scale_ti = 1
if 'scale' in targets_df_gi.columns:
scale_ti = targets_df_gi['scale'].iloc[ti]
if options.restart and os.path.isfile(seqs_cov_file):
print('Skipping existing %s' % seqs_cov_file, file=sys.stderr)
else:
cmd = 'basenji_data_read.py'
cmd += ' --crop %d' % options.crop_bp
cmd += ' -u %s' % targets_df_gi['sum_stat'].iloc[ti]
cmd += ' -w %d' % options.pool_width
if clip_ti is not None:
cmd += ' -c %f' % clip_ti
if options.soft_clip:
cmd += ' --soft'
cmd += ' -s %f' % scale_ti
if options.blacklist_beds[gi]:
cmd += ' -b %s' % options.blacklist_beds[gi]
if options.interp_nan:
cmd += ' -i'
cmd += ' %s' % genome_cov_file
cmd += ' %s' % seqs_bed_file
cmd += ' %s' % seqs_cov_file
if options.run_local:
cmd += ' &> %s.err' % seqs_cov_stem
read_jobs.append(cmd)
else:
j = slurm.Job(cmd,
name='read_t%d' % ti,
out_file='%s.out' % seqs_cov_stem,
err_file='%s.err' % seqs_cov_stem,
queue='standard', mem=15000, time='12:0:0')
read_jobs.append(j)
return read_jobs
def test_train(self):
if os.path.isdir(self.exp_dir):
shutil.rmtree(self.exp_dir)
os.mkdir(self.exp_dir)
################################################################
# basenji test
################################################################
basenji_cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
basenji_cmd += ' conda activate %s;' % self.conda_env
basenji_cmd += ' basenji_test.py'
basenji_cmd += ' -o %s' % self.exp_dir
basenji_cmd += ' --rc'
basenji_cmd += ' --shifts "1,0,-1"'
basenji_cmd += ' %s' % self.params_file
basenji_cmd += ' %s' % self.model_file
basenji_cmd += ' %s' % self.data_dir
basenji_job = slurm.Job(basenji_cmd,
name='test_test',
out_file='%s/test.out'%self.exp_dir,
err_file='%s/test.err'%self.exp_dir,
queue=self.queue,
cpu=1,
gpu=1,
mem=23000,
time='1:00:00')
slurm.multi_run([basenji_job], verbose=True)
################################################################
# compare
################################################################
if os.path.isfile(self.ref_acc_file):
ref_df = pd.read_csv(self.ref_acc_file, sep='\t', index_col=0)
exp_acc_file = '%s/acc.txt' % self.exp_dir
exp_df = pd.read_csv(exp_acc_file, sep='\t', index_col=0)
np.testing.assert_allclose(ref_df.pearsonr, exp_df.pearsonr, atol=1e-3, rtol=1e-3)
np.testing.assert_allclose(ref_df.r2, exp_df.r2, atol=1e-3, rtol=1e-3)
else:
print('Moving experiment to reference.')
os.rename(self.exp_dir, os.path.split(self.ref_acc_file)[0])
def make_write_jobs(
mseqs,
fasta_file,
seqs_bed_file,
seqs_cov_dir,
tfr_dir,
gi,
unmap_npy,
targets_start,
sum_targets,
options,
):
"""Make basenji_data_write.py jobs for one genome."""
write_jobs = []
for tvt_set in ["train", "valid", "test"]:
tvt_set_indexes = [i for i in range(len(mseqs)) if mseqs[i].label == tvt_set]
tvt_set_start = tvt_set_indexes[0]
tvt_set_end = tvt_set_indexes[-1] + 1
tfr_i = 0
tfr_start = tvt_set_start
tfr_end = min(tfr_start + options.seqs_per_tfr, tvt_set_end)
while tfr_start <= tvt_set_end:
tfr_stem = "%s/%s-%d-%d" % (tfr_dir, tvt_set, gi, tfr_i)
cmd = "basenji_data_write.py"
cmd += " -s %d" % tfr_start
cmd += " -e %d" % tfr_end
cmd += " -g %d" % gi
cmd += " --ts %d" % targets_start
cmd += " --te %d" % sum_targets
if unmap_npy is not None:
cmd += " -u %s" % unmap_npy
if options.umap_set is not None:
cmd += " --umap_set %f" % options.umap_set
cmd += " %s" % fasta_file
cmd += " %s" % seqs_bed_file
cmd += " %s" % seqs_cov_dir
cmd += " %s.tfr" % tfr_stem
if options.run_local:
cmd += " &> %s.err" % tfr_stem
write_jobs.append(cmd)
else:
j = slurm.Job(
cmd,
name="write_%s-%d" % (tvt_set, tfr_i),
out_file="%s.out" % tfr_stem,
err_file="%s.err" % tfr_stem,
queue="standard",
mem=15000,
time="12:0:0",
)
write_jobs.append(j)
# update
tfr_i += 1
tfr_start += options.seqs_per_tfr
tfr_end = min(tfr_start + options.seqs_per_tfr, tvt_set_end)
return write_jobs
def main():
usage = 'usage: %prog [options] <params_file> <model_file> <vcf_file>'
parser = OptionParser(usage)
# sad
parser.add_option(
'-c',
dest='center_pct',
default=0.25,
type='float',
help='Require clustered SNPs lie in center region [Default: %default]')
parser.add_option('-f',
dest='genome_fasta',
default='%s/data/hg19.fa' % os.environ['BASENJIDIR'],
help='Genome FASTA for sequences [Default: %default]')
parser.add_option('-g',
dest='genome_file',
default='%s/data/human.hg19.genome' %
os.environ['BASENJIDIR'],
help='Chromosome lengths file [Default: %default]')
parser.add_option('--h5',
dest='out_h5',
default=False,
action='store_true',
help='Output stats to sad.h5 [Default: %default]')
parser.add_option('--local',
dest='local',
default=1024,
type='int',
help='Local SAD score [Default: %default]')
parser.add_option('-n',
dest='norm_file',
default=None,
help='Normalize SAD scores')
parser.add_option(
'-o',
dest='out_dir',
default='sad',
help='Output directory for tables and plots [Default: %default]')
parser.add_option('--pseudo',
dest='log_pseudo',
default=1,
type='float',
help='Log2 pseudocount [Default: %default]')
parser.add_option(
'--rc',
dest='rc',
default=False,
action='store_true',
help=
'Average forward and reverse complement predictions [Default: %default]'
)
parser.add_option('--shifts',
dest='shifts',
default='0',
type='str',
help='Ensemble prediction shifts [Default: %default]')
parser.add_option(
'--stats',
dest='sad_stats',
default='SAD',
help='Comma-separated list of stats to save. [Default: %default]')
parser.add_option(
'-t',
dest='targets_file',
default=None,
type='str',
help='File specifying target indexes and labels in table format')
parser.add_option(
'--ti',
dest='track_indexes',
default=None,
type='str',
help='Comma-separated list of target indexes to output BigWig tracks')
parser.add_option(
'-u',
dest='penultimate',
default=False,
action='store_true',
help='Compute SED in the penultimate layer [Default: %default]')
parser.add_option('-z',
dest='out_zarr',
default=False,
action='store_true',
help='Output stats to sad.zarr [Default: %default]')
# multi
parser.add_option('--name',
dest='name',
default='sad',
help='SLURM name prefix [Default: %default]')
parser.add_option('-p',
dest='processes',
default=None,
type='int',
help='Number of processes, passed by multi script')
parser.add_option(
'-q',
dest='queue',
default='k80',
help='SLURM queue on which to run the jobs [Default: %default]')
parser.add_option(
'-r',
dest='restart',
default=False,
action='store_true',
help='Restart a partially completed job [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 3:
parser.error('Must provide parameters and model files and VCF file')
else:
params_file = args[0]
model_file = args[1]
vcf_file = args[2]
#######################################################
# prep work
# output directory
if not options.restart:
if os.path.isdir(options.out_dir):
print('Please remove %s' % options.out_dir, file=sys.stderr)
exit(1)
os.mkdir(options.out_dir)
# pickle options
options_pkl_file = '%s/options.pkl' % options.out_dir
options_pkl = open(options_pkl_file, 'wb')
pickle.dump(options, options_pkl)
options_pkl.close()
#######################################################
# launch worker threads
jobs = []
for pi in range(options.processes):
if not options.restart or not job_completed(options, pi):
cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
cmd += ' conda activate tf1.13-gpu;'
cmd += ' echo $HOSTNAME;'
cmd += ' basenji_sad_ref.py %s %s %d' % (options_pkl_file,
' '.join(args), pi)
name = '%s_p%d' % (options.name, pi)
outf = '%s/job%d.out' % (options.out_dir, pi)
errf = '%s/job%d.err' % (options.out_dir, pi)
j = slurm.Job(cmd,
name,
outf,
errf,
queue=options.queue,
gpu=1,
mem=37000,
time='7-0:0:0')
jobs.append(j)
slurm.multi_run(jobs,
max_proc=options.processes,
verbose=True,
launch_sleep=10,
update_sleep=60)
#######################################################
# collect output
if options.out_h5:
collect_h5('sad.h5', options.out_dir, options.processes)
elif options.out_zarr:
collect_zarr('sad.zarr', options.out_dir, options.processes)
else:
collect_table('sad_table.txt', options.out_dir, options.processes)
def main():
usage = 'usage: %prog [options] <params_file> <data1_dir> ...'
parser = OptionParser(usage)
# train
train_options = OptionGroup(parser, 'basenji_train.py options')
train_options.add_option(
'-k',
dest='keras_fit',
default=False,
action='store_true',
help='Train with Keras fit method [Default: %default]')
train_options.add_option(
'-o',
dest='out_dir',
default='train_out',
help='Output directory for test statistics [Default: %default]')
train_options.add_option(
'--restore',
dest='restore',
help=
'Restore model and continue training, from existing fold train dir [Default: %default]'
)
train_options.add_option(
'--trunk',
dest='trunk',
default=False,
action='store_true',
help='Restore only model trunk [Default: %default]')
train_options.add_option(
'--tfr_train',
dest='tfr_train_pattern',
default=None,
help=
'Training TFR pattern string appended to data_dir/tfrecords for subsetting [Default: %default]'
)
train_options.add_option(
'--tfr_eval',
dest='tfr_eval_pattern',
default=None,
help=
'Evaluation TFR pattern string appended to data_dir/tfrecords for subsetting [Default: %default]'
)
parser.add_option_group(train_options)
# test
test_options = OptionGroup(parser, 'basenji_test.py options')
test_options.add_option(
'--rc',
dest='rc',
default=False,
action='store_true',
help=
'Average forward and reverse complement predictions [Default: %default]'
)
test_options.add_option(
'--shifts',
dest='shifts',
default='0',
type='str',
help='Ensemble prediction shifts [Default: %default]')
parser.add_option_group(test_options)
# multi
rep_options = OptionGroup(parser, 'replication options')
rep_options.add_option(
'-c',
dest='crosses',
default=1,
type='int',
help='Number of cross-fold rounds [Default:%default]')
rep_options.add_option('-e',
dest='conda_env',
default='tf2.4',
help='Anaconda environment [Default: %default]')
rep_options.add_option('-f',
dest='fold_subset',
default=None,
type='int',
help='Run a subset of folds [Default:%default]')
rep_options.add_option('--name',
dest='name',
default='fold',
help='SLURM name prefix [Default: %default]')
rep_options.add_option('-p',
dest='processes',
default=None,
type='int',
help='Number of processes, passed by multi script')
rep_options.add_option(
'-q',
dest='queue',
default='gtx1080ti',
help='SLURM queue on which to run the jobs [Default: %default]')
rep_options.add_option('-r',
dest='restart',
default=False,
action='store_true')
rep_options.add_option('--spec_off',
dest='spec_off',
default=False,
action='store_true')
rep_options.add_option('--test_off',
dest='test_off',
default=False,
action='store_true')
rep_options.add_option('--test_train_off',
dest='test_train_off',
default=False,
action='store_true')
parser.add_option_group(rep_options)
(options, args) = parser.parse_args()
if len(args) < 2:
parser.error('Must provide parameters and data directory.')
else:
params_file = os.path.abspath(args[0])
data_dirs = [os.path.abspath(arg) for arg in args[1:]]
# read model parameters
with open(params_file) as params_open:
params = json.load(params_open)
params_train = params['train']
#######################################################
# prep work
if not options.restart and os.path.isdir(options.out_dir):
print('Output directory %s exists. Please remove.' % options.out_dir)
exit(1)
if not os.path.isdir(options.out_dir):
os.mkdir(options.out_dir)
# read data parameters
num_data = len(data_dirs)
data_stats_file = '%s/statistics.json' % data_dirs[0]
with open(data_stats_file) as data_stats_open:
data_stats = json.load(data_stats_open)
# count folds
num_folds = len([dkey for dkey in data_stats if dkey.startswith('fold')])
# subset folds
if options.fold_subset is not None:
num_folds = min(options.fold_subset, num_folds)
#######################################################
# train
jobs = []
for ci in range(options.crosses):
for fi in range(num_folds):
rep_dir = '%s/f%d_c%d' % (options.out_dir, fi, ci)
if options.restart and os.path.isdir(rep_dir):
print('%s found and skipped.' % rep_dir)
else:
# make rep dir
os.mkdir(rep_dir)
# make rep data
rep_data_dirs = []
for di in range(num_data):
rep_data_dirs.append('%s/data%d' % (rep_dir, di))
make_rep_data(data_dirs[di], rep_data_dirs[-1], fi, ci)
# train command
cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
cmd += ' conda activate %s;' % options.conda_env
cmd += ' echo $HOSTNAME;'
cmd += ' basenji_train.py'
cmd += ' %s' % options_string(options, train_options, rep_dir)
cmd += ' %s %s' % (params_file, ' '.join(rep_data_dirs))
name = '%s-train-f%dc%d' % (options.name, fi, ci)
sbf = os.path.abspath('%s/train.sb' % rep_dir)
outf = os.path.abspath('%s/train.out' % rep_dir)
errf = os.path.abspath('%s/train.err' % rep_dir)
j = slurm.Job(cmd,
name,
outf,
errf,
sbf,
queue=options.queue,
cpu=4,
gpu=params_train.get('num_gpu', 1),
mem=37000,
time='28-0:0:0')
jobs.append(j)
slurm.multi_run(jobs,
max_proc=options.processes,
verbose=True,
launch_sleep=10,
update_sleep=60)
#######################################################
# test train
jobs = []
if not options.test_train_off:
for ci in range(options.crosses):
for fi in range(num_folds):
it_dir = '%s/f%d_c%d' % (options.out_dir, fi, ci)
for di in range(num_data):
if num_data == 1:
out_dir = '%s/test_train' % it_dir
model_file = '%s/train/model_check.h5' % it_dir
else:
out_dir = '%s/test%d_train' % (it_dir, di)
model_file = '%s/train/model%d_check.h5' % (it_dir, di)
# check if done
acc_file = '%s/acc.txt' % out_dir
if os.path.isfile(acc_file):
print('%s already generated.' % acc_file)
else:
# basenji test
basenji_cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
basenji_cmd += ' conda activate %s;' % options.conda_env
basenji_cmd += ' basenji_test.py'
basenji_cmd += ' --head %d' % di
basenji_cmd += ' -o %s' % out_dir
if options.rc:
basenji_cmd += ' --rc'
if options.shifts:
basenji_cmd += ' --shifts %s' % options.shifts
basenji_cmd += ' --split train'
basenji_cmd += ' %s' % params_file
basenji_cmd += ' %s' % model_file
basenji_cmd += ' %s/data%d' % (it_dir, di)
name = '%s-testtr-f%dc%d' % (options.name, fi, ci)
basenji_job = slurm.Job(basenji_cmd,
name=name,
out_file='%s.out' % out_dir,
err_file='%s.err' % out_dir,
queue=options.queue,
cpu=1,
gpu=1,
mem=23000,
time='8:00:00')
jobs.append(basenji_job)
#######################################################
# test best
if not options.test_off:
for ci in range(options.crosses):
for fi in range(num_folds):
it_dir = '%s/f%d_c%d' % (options.out_dir, fi, ci)
for di in range(num_data):
if num_data == 1:
out_dir = '%s/test' % it_dir
model_file = '%s/train/model_best.h5' % it_dir
else:
out_dir = '%s/test%d' % (it_dir, di)
model_file = '%s/train/model%d_best.h5' % (it_dir, di)
# check if done
acc_file = '%s/acc.txt' % out_dir
if os.path.isfile(acc_file):
print('%s already generated.' % acc_file)
else:
# basenji test
basenji_cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
basenji_cmd += ' conda activate %s;' % options.conda_env
basenji_cmd += ' basenji_test.py'
basenji_cmd += ' --head %d' % di
basenji_cmd += ' -o %s' % out_dir
if options.rc:
basenji_cmd += ' --rc'
if options.shifts:
basenji_cmd += ' --shifts %s' % options.shifts
basenji_cmd += ' %s' % params_file
basenji_cmd += ' %s' % model_file
basenji_cmd += ' %s/data%d' % (it_dir, di)
name = '%s-test-f%dc%d' % (options.name, fi, ci)
basenji_job = slurm.Job(basenji_cmd,
name=name,
out_file='%s.out' % out_dir,
err_file='%s.err' % out_dir,
queue=options.queue,
cpu=1,
gpu=1,
mem=23000,
time='4:00:00')
jobs.append(basenji_job)
#######################################################
# test best specificity
if not options.spec_off:
for ci in range(options.crosses):
for fi in range(num_folds):
it_dir = '%s/f%d_c%d' % (options.out_dir, fi, ci)
for di in range(num_data):
if num_data == 1:
out_dir = '%s/test_spec' % it_dir
model_file = '%s/train/model_best.h5' % it_dir
else:
out_dir = '%s/test%d_spec' % (it_dir, di)
model_file = '%s/train/model%d_best.h5' % (it_dir, di)
# check if done
acc_file = '%s/acc.txt' % out_dir
if os.path.isfile(acc_file):
print('%s already generated.' % acc_file)
else:
# basenji test
basenji_cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
basenji_cmd += ' conda activate %s;' % options.conda_env
basenji_cmd += ' basenji_test_specificity.py'
basenji_cmd += ' --head %d' % di
basenji_cmd += ' -o %s' % out_dir
if options.rc:
basenji_cmd += ' --rc'
if options.shifts:
basenji_cmd += ' --shifts %s' % options.shifts
basenji_cmd += ' %s' % params_file
basenji_cmd += ' %s' % model_file
basenji_cmd += ' %s/data%d' % (it_dir, di)
name = '%s-spec-f%dc%d' % (options.name, fi, ci)
basenji_job = slurm.Job(basenji_cmd,
name=name,
out_file='%s.out' % out_dir,
err_file='%s.err' % out_dir,
queue=options.queue,
cpu=1,
gpu=1,
mem=90000,
time='6:00:00')
jobs.append(basenji_job)
slurm.multi_run(jobs,
max_proc=options.processes,
verbose=True,
launch_sleep=10,
update_sleep=60)
def main():
usage = 'usage: %prog [options] <params_file> <model_file> <bed_file>'
parser = OptionParser(usage)
# basenji_predict_bed.py options
parser.add_option(
'-b',
dest='bigwig_indexes',
default=None,
help='Comma-separated list of target indexes to write BigWigs')
parser.add_option('-e',
dest='embed_layer',
default=None,
type='int',
help='Embed sequences using the specified layer index.')
parser.add_option('-f',
dest='genome_fasta',
default=None,
help='Genome FASTA for sequences [Default: %default]')
parser.add_option('-g',
dest='genome_file',
default=None,
help='Chromosome length information [Default: %default]')
parser.add_option(
'-l',
dest='site_length',
default=None,
type='int',
help='Prediction site length. [Default: params.seq_length]')
parser.add_option('-o',
dest='out_dir',
default='pred_out',
help='Output directory [Default: %default]')
parser.add_option(
'--rc',
dest='rc',
default=False,
action='store_true',
help=
'Ensemble forward and reverse complement predictions [Default: %default]'
)
parser.add_option('-s',
dest='sum',
default=False,
action='store_true',
help='Sum site predictions [Default: %default]')
parser.add_option('--shifts',
dest='shifts',
default='0',
help='Ensemble prediction shifts [Default: %default]')
parser.add_option(
'-t',
dest='targets_file',
default=None,
type='str',
help='File specifying target indexes and labels in table format')
# _multi.py options
parser.add_option('-p',
dest='processes',
default=None,
type='int',
help='Number of processes, passed by multi script')
parser.add_option(
'-q',
dest='queue',
default='gtx1080ti',
help='SLURM queue on which to run the jobs [Default: %default]')
parser.add_option(
'-r',
dest='restart',
default=False,
action='store_true',
help='Restart a partially completed job [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 3:
print(args)
parser.error('Must provide parameters and model files and BED file')
else:
params_file = args[0]
model_file = args[1]
bed_file = args[2]
#######################################################
# prep work
# output directory
if not options.restart:
if os.path.isdir(options.out_dir):
print('Please remove %s' % options.out_dir, file=sys.stderr)
exit(1)
os.mkdir(options.out_dir)
# pickle options
options_pkl_file = '%s/options.pkl' % options.out_dir
options_pkl = open(options_pkl_file, 'wb')
pickle.dump(options, options_pkl)
options_pkl.close()
#######################################################
# launch worker threads
jobs = []
for pi in range(options.processes):
if not options.restart or not job_completed(options, pi):
cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
cmd += ' conda activate tf1.15-gpu;'
cmd += ' basenji_predict_bed.py %s %s %d' % (options_pkl_file,
' '.join(args), pi)
name = 'pred_p%d' % pi
outf = '%s/job%d.out' % (options.out_dir, pi)
errf = '%s/job%d.err' % (options.out_dir, pi)
j = slurm.Job(cmd,
name,
outf,
errf,
queue=options.queue,
gpu=1,
mem=60000,
time='14-0:0:0')
jobs.append(j)
slurm.multi_run(jobs,
max_proc=options.processes,
verbose=True,
launch_sleep=10,
update_sleep=60)
#######################################################
# collect output
collect_h5(options.out_dir, options.processes)
def test_train(self):
exp_dir = 'train_full/exp'
if os.path.isdir(exp_dir):
shutil.rmtree(exp_dir)
os.mkdir(exp_dir)
################################################################
# train
################################################################
jobs = []
for i in range(self.iterations):
it_dir = '%s/%d' % (exp_dir, i)
os.mkdir(it_dir)
# basenji train
basenji_cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
basenji_cmd += ' conda activate %s;' % self.conda_env
basenji_cmd += ' %s/basenji_train.py' % self.basenji_path
basenji_cmd += ' -o %s/train' % it_dir
basenji_cmd += ' %s' % self.params_file
basenji_cmd += ' %s' % self.data_dir
basenji_job = slurm.Job(basenji_cmd,
name='train%d' % i,
out_file='%s/train.out'%it_dir,
err_file='%s/train.err'%it_dir,
queue=self.queue,
cpu=1,
gpu=1,
mem=23000,
time='12-00:00:00')
jobs.append(basenji_job)
slurm.multi_run(jobs, verbose=True)
################################################################
# test check
################################################################
jobs = []
for i in range(self.iterations):
it_dir = '%s/%d' % (exp_dir, i)
# basenji test
basenji_cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
basenji_cmd += ' conda activate %s;' % self.conda_env
basenji_cmd += ' %s/basenji_test.py' % self.basenji_path
basenji_cmd += ' -o %s/test_train' % it_dir
basenji_cmd += ' --tfr "train-*.tfr"'
basenji_cmd += ' %s' % self.params_file
basenji_cmd += ' %s/train/model_check.h5' % it_dir
basenji_cmd += ' %s' % self.data_dir
basenji_job = slurm.Job(basenji_cmd,
name='test%d' % i,
out_file='%s/test_train.out'%it_dir,
err_file='%s/test_train.err'%it_dir,
queue=self.queue,
cpu=1,
gpu=1,
mem=23000,
time='4:00:00')
jobs.append(basenji_job)
slurm.multi_run(jobs, verbose=True)
################################################################
# test best
################################################################
jobs = []
for i in range(self.iterations):
it_dir = '%s/%d' % (exp_dir, i)
# basenji test
basenji_cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
basenji_cmd += ' conda activate %s;' % self.conda_env
basenji_cmd += ' %s/basenji_test.py' % self.basenji_path
basenji_cmd += ' -o %s/test' % it_dir
basenji_cmd += ' %s' % self.params_file
basenji_cmd += ' %s/train/model_best.h5' % it_dir
basenji_cmd += ' %s' % self.data_dir
basenji_job = slurm.Job(basenji_cmd,
name='test%d' % i,
out_file='%s/test.out'%it_dir,
err_file='%s/test.err'%it_dir,
queue=self.queue,
cpu=1,
gpu=1,
mem=23000,
time='4:00:00')
jobs.append(basenji_job)
slurm.multi_run(jobs, verbose=True)
################################################################
# compare checkpoint on training set
################################################################
ref_cors = []
for acc_file in glob.glob('%s/*/test_train/acc.txt' % self.ref_dir):
acc_df = pd.read_csv(acc_file, sep='\t', index_col=0)
ref_cors.append(acc_df.pearsonr.mean())
exp_cors = []
for acc_file in glob.glob('%s/*/test_train/acc.txt' % exp_dir):
acc_df = pd.read_csv(acc_file, sep='\t', index_col=0)
exp_cors.append(acc_df.pearsonr.mean())
_, mwp = mannwhitneyu(ref_cors, exp_cors, alternative='two-sided')
_, tp = ttest_ind(ref_cors, exp_cors)
print('\nTrain:')
print('Reference PearsonR: %.4f (%.4f)' % (np.mean(ref_cors), np.std(ref_cors)))
print('Experiment PearsonR: %.4f (%.4f)' % (np.mean(exp_cors), np.std(exp_cors)))
print('Mann-Whitney U p-value: %.3g' % mwp)
print('T-test p-value: %.3g' % tp)
# self.assertGreater(mwp, 0.05)
# self.assertGreater(tp, 0.05)
################################################################
# compare best on test set
################################################################
ref_cors = []
for acc_file in glob.glob('%s/*/test/acc.txt' % self.ref_dir):
acc_df = pd.read_csv(acc_file, sep='\t', index_col=0)
ref_cors.append(acc_df.pearsonr.mean())
exp_cors = []
for acc_file in glob.glob('%s/*/test/acc.txt' % exp_dir):
acc_df = pd.read_csv(acc_file, sep='\t', index_col=0)
exp_cors.append(acc_df.pearsonr.mean())
_, mwp = mannwhitneyu(ref_cors, exp_cors, alternative='two-sided')
_, tp = ttest_ind(ref_cors, exp_cors)
print('\nTest:')
print('Reference PearsonR: %.4f (%.4f)' % (np.mean(ref_cors), np.std(ref_cors)))
print('Experiment PearsonR: %.4f (%.4f)' % (np.mean(exp_cors), np.std(exp_cors)))
print('Mann-Whitney U p-value: %.3g' % mwp)
print('T-test p-value: %.3g' % tp)
def main():
usage = 'usage: %prog [options] <fasta_file> <targets_file>'
parser = OptionParser(usage)
parser.add_option('-b',
dest='blacklist_bed',
help='Set blacklist nucleotides to a baseline value.')
parser.add_option(
'--break',
dest='break_t',
default=8388608,
type='int',
help='Break in half contigs above length [Default: %default]')
parser.add_option('--crop',
dest='crop_bp',
default=0,
type='int',
help='Crop bp off each end [Default: %default]')
parser.add_option(
'-d',
dest='diagonal_offset',
default=2,
type='int',
help='Positions on the diagonal to ignore [Default: %default]')
parser.add_option('-g',
dest='gaps_file',
help='Genome assembly gaps BED [Default: %default]')
parser.add_option(
'-k',
dest='kernel_stddev',
default=0,
type='int',
help='Gaussian kernel stddev to smooth values [Default: %default]')
parser.add_option('-l',
dest='seq_length',
default=131072,
type='int',
help='Sequence length [Default: %default]')
parser.add_option(
'--limit',
dest='limit_bed',
help='Limit to segments that overlap regions in a BED file')
parser.add_option(
'--local',
dest='run_local',
default=False,
action='store_true',
help='Run jobs locally as opposed to on SLURM [Default: %default]')
parser.add_option('-o',
dest='out_dir',
default='data_out',
help='Output directory [Default: %default]')
parser.add_option('-p',
dest='processes',
default=None,
type='int',
help='Number parallel processes [Default: %default]')
parser.add_option('-r',
dest='seqs_per_tfr',
default=128,
type='int',
help='Sequences per TFRecord file [Default: %default]')
parser.add_option(
'--restart',
dest='restart',
default=False,
action='store_true',
help='Skip already read HDF5 coverage values. [Default: %default]')
parser.add_option('--sample',
dest='sample_pct',
default=1.0,
type='float',
help='Down-sample the segments')
parser.add_option('--seed',
dest='seed',
default=44,
type='int',
help='Random seed [Default: %default]')
parser.add_option(
'--stride_train',
dest='stride_train',
default=1.,
type='float',
help='Stride to advance train sequences [Default: seq_length]')
parser.add_option(
'--stride_test',
dest='stride_test',
default=1.,
type='float',
help='Stride to advance valid and test sequences [Default: seq_length]'
)
parser.add_option(
'--soft',
dest='soft_clip',
default=False,
action='store_true',
help=
'Soft clip values, applying sqrt to the execess above the threshold [Default: %default]'
)
parser.add_option(
'-t',
dest='test_pct_or_chr',
default=0.05,
type='str',
help='Proportion of the data for testing [Default: %default]')
parser.add_option('-u',
dest='umap_bed',
help='Unmappable regions in BED format')
parser.add_option(
'--umap_midpoints',
dest='umap_midpoints',
help='Regions with midpoints to exclude in BED format. Used for 4C/HiC.'
)
parser.add_option(
'--umap_t',
dest='umap_t',
default=0.3,
type='float',
help=
'Remove sequences with more than this unmappable bin % [Default: %default]'
)
parser.add_option(
'--umap_set',
dest='umap_set',
default=None,
type='float',
help=
'Set unmappable regions to this percentile in the sequences\' distribution of values'
)
parser.add_option('-w',
dest='pool_width',
default=128,
type='int',
help='Sum pool width [Default: %default]')
parser.add_option(
'-v',
dest='valid_pct_or_chr',
default=0.05,
type='str',
help='Proportion of the data for validation [Default: %default]')
parser.add_option(
'--snap',
dest='snap',
default=None,
type='int',
help=
'snap stride to multiple for binned targets in bp, if not None seq_length must be a multiple of snap'
)
parser.add_option('--as_obsexp',
dest='as_obsexp',
action="store_true",
default=False,
help='save targets as obsexp profiles')
parser.add_option('--global_obsexp',
dest='global_obsexp',
action="store_true",
default=False,
help='use pre-calculated by-chromosome obs/exp')
parser.add_option('--no_log',
dest='no_log',
action="store_true",
default=False,
help='do not take log for obs/exp')
(options, args) = parser.parse_args()
if len(args) != 2:
parser.error(
'Must provide FASTA and sample coverage labels and paths.')
else:
fasta_file = args[0]
targets_file = args[1]
random.seed(options.seed)
np.random.seed(options.seed)
# transform proportion strides to base pairs
if options.stride_train <= 1:
print('stride_train %.f' % options.stride_train, end='')
options.stride_train = options.stride_train * options.seq_length
print(' converted to %f' % options.stride_train)
options.stride_train = int(np.round(options.stride_train))
if options.stride_test <= 1:
print('stride_test %.f' % options.stride_test, end='')
options.stride_test = options.stride_test * options.seq_length
print(' converted to %f' % options.stride_test)
options.stride_test = int(np.round(options.stride_test))
if options.snap != None:
if np.mod(options.seq_length, options.snap) != 0:
raise ValueError('seq_length must be a multiple of snap')
if np.mod(options.stride_train, options.snap) != 0:
raise ValueError('stride_train must be a multiple of snap')
if np.mod(options.stride_test, options.snap) != 0:
raise ValueError('stride_test must be a multiple of snap')
if os.path.isdir(options.out_dir) and not options.restart:
print('Remove output directory %s or use --restart option.' %
options.out_dir)
exit(1)
elif not os.path.isdir(options.out_dir):
os.mkdir(options.out_dir)
# dump options
with open('%s/options.json' % options.out_dir, 'w') as options_json_out:
json.dump(options.__dict__, options_json_out, sort_keys=True, indent=4)
################################################################
# define genomic contigs
################################################################
chrom_contigs = genome.load_chromosomes(fasta_file)
# remove gaps
if options.gaps_file:
chrom_contigs = genome.split_contigs(chrom_contigs, options.gaps_file)
# ditch the chromosomes for contigs
contigs = []
for chrom in chrom_contigs:
contigs += [
Contig(chrom, ctg_start, ctg_end)
for ctg_start, ctg_end in chrom_contigs[chrom]
]
# limit to a BED file
if options.limit_bed is not None:
contigs = limit_contigs(contigs, options.limit_bed)
# filter for large enough
contigs = [
ctg for ctg in contigs if ctg.end - ctg.start >= options.seq_length
]
# break up large contigs
if options.break_t is not None:
contigs = break_large_contigs(contigs, options.break_t)
# print contigs to BED file
ctg_bed_file = '%s/contigs.bed' % options.out_dir
write_seqs_bed(ctg_bed_file, contigs)
################################################################
# divide between train/valid/test
################################################################
try:
# convert to float pct
valid_pct = float(options.valid_pct_or_chr)
test_pct = float(options.test_pct_or_chr)
assert (0 <= valid_pct <= 1)
assert (0 <= test_pct <= 1)
# divide by pct
contig_sets = divide_contigs_pct(contigs, test_pct, valid_pct)
except (ValueError, AssertionError):
# divide by chr
valid_chrs = options.valid_pct_or_chr.split(',')
test_chrs = options.test_pct_or_chr.split(',')
contig_sets = divide_contigs_chr(contigs, test_chrs, valid_chrs)
train_contigs, valid_contigs, test_contigs = contig_sets
# rejoin broken contigs within set
train_contigs = rejoin_large_contigs(train_contigs)
valid_contigs = rejoin_large_contigs(valid_contigs)
test_contigs = rejoin_large_contigs(test_contigs)
################################################################
# define model sequences
################################################################
# stride sequences across contig
train_mseqs = contig_sequences(train_contigs,
options.seq_length,
options.stride_train,
options.snap,
label='train')
valid_mseqs = contig_sequences(valid_contigs,
options.seq_length,
options.stride_test,
options.snap,
label='valid')
test_mseqs = contig_sequences(test_contigs,
options.seq_length,
options.stride_test,
options.snap,
label='test')
# shuffle
random.shuffle(train_mseqs)
random.shuffle(valid_mseqs)
random.shuffle(test_mseqs)
# down-sample
if options.sample_pct < 1.0:
train_mseqs = random.sample(train_mseqs,
int(options.sample_pct * len(train_mseqs)))
valid_mseqs = random.sample(valid_mseqs,
int(options.sample_pct * len(valid_mseqs)))
test_mseqs = random.sample(test_mseqs,
int(options.sample_pct * len(test_mseqs)))
# merge
mseqs = train_mseqs + valid_mseqs + test_mseqs
################################################################
# mappability
################################################################
if (options.umap_bed is not None) or (options.umap_midpoints is not None):
if shutil.which('bedtools') is None:
print('Install Bedtools to annotate unmappable sites',
file=sys.stderr)
exit(1)
if options.umap_bed is not None:
# annotate unmappable positions
mseqs_unmap = annotate_unmap(mseqs, options.umap_bed,
options.seq_length, options.pool_width)
# filter unmappable
mseqs_map_mask = (mseqs_unmap.mean(axis=1, dtype='float64') <
options.umap_t)
mseqs = [mseqs[i] for i in range(len(mseqs)) if mseqs_map_mask[i]]
mseqs_unmap = mseqs_unmap[mseqs_map_mask, :]
# write to file
unmap_npy = '%s/mseqs_unmap.npy' % options.out_dir
np.save(unmap_npy, mseqs_unmap)
if options.umap_midpoints is not None:
# annotate unmappable midpoints for 4C/HiC
mseqs_unmap = annotate_unmap(mseqs, options.umap_midpoints,
options.seq_length, options.pool_width)
# filter unmappable
seqmid = mseqs_unmap.shape[
1] // 2 #int( options.seq_length / options.pool_width /2)
mseqs_map_mask = (np.sum(mseqs_unmap[:, seqmid - 1:seqmid + 1],
axis=1) == 0)
mseqs = [mseqs[i] for i in range(len(mseqs)) if mseqs_map_mask[i]]
mseqs_unmap = mseqs_unmap[mseqs_map_mask, :]
# write to file
unmap_npy = '%s/mseqs_unmap_midpoints.npy' % options.out_dir
np.save(unmap_npy, mseqs_unmap)
# write sequences to BED
print('writing sequences to BED')
seqs_bed_file = '%s/sequences.bed' % options.out_dir
write_seqs_bed(seqs_bed_file, mseqs, True)
################################################################
# read sequence coverage values
################################################################
# read target datasets
targets_df = pd.read_csv(targets_file, index_col=0, sep='\t')
seqs_cov_dir = '%s/seqs_cov' % options.out_dir
if not os.path.isdir(seqs_cov_dir):
os.mkdir(seqs_cov_dir)
read_jobs = []
for ti in range(targets_df.shape[0]):
genome_cov_file = targets_df['file'].iloc[ti]
seqs_cov_stem = '%s/%d' % (seqs_cov_dir, ti)
seqs_cov_file = '%s.h5' % seqs_cov_stem
clip_ti = None
if 'clip' in targets_df.columns:
clip_ti = targets_df['clip'].iloc[ti]
# scale_ti = 1
# if 'scale' in targets_df.columns:
# scale_ti = targets_df['scale'].iloc[ti]
if options.restart and os.path.isfile(seqs_cov_file):
print('Skipping existing %s' % seqs_cov_file, file=sys.stderr)
else:
cmd = 'akita_data_read.py'
cmd += ' --crop %d' % options.crop_bp
cmd += ' -k %d' % options.kernel_stddev
cmd += ' -w %d' % options.pool_width
if clip_ti is not None:
cmd += ' --clip %f' % clip_ti
if options.soft_clip:
cmd += ' --soft'
# cmd += ' -s %f' % scale_ti
if options.blacklist_bed:
cmd += ' -b %s' % options.blacklist_bed
if options.as_obsexp:
cmd += ' --as_obsexp'
if options.global_obsexp:
cmd += ' --global_obsexp'
if options.no_log:
cmd += ' --no_log'
cmd += ' %s' % genome_cov_file
cmd += ' %s' % seqs_bed_file
cmd += ' %s' % seqs_cov_file
if options.run_local:
# breaks on some OS
# cmd += ' &> %s.err' % seqs_cov_stem
read_jobs.append(cmd)
else:
j = slurm.Job(cmd,
name='read_t%d' % ti,
out_file='%s.out' % seqs_cov_stem,
err_file='%s.err' % seqs_cov_stem,
queue='standard',
mem=15000,
time='12:0:0')
read_jobs.append(j)
if options.run_local:
util.exec_par(read_jobs, options.processes, verbose=True)
else:
slurm.multi_run(read_jobs,
options.processes,
verbose=True,
launch_sleep=1,
update_sleep=5)
################################################################
# write TF Records
################################################################
# copy targets file
shutil.copy(targets_file, '%s/targets.txt' % options.out_dir)
# initialize TF Records dir
tfr_dir = '%s/tfrecords' % options.out_dir
if not os.path.isdir(tfr_dir):
os.mkdir(tfr_dir)
write_jobs = []
for tvt_set in ['train', 'valid', 'test']:
tvt_set_indexes = [
i for i in range(len(mseqs)) if mseqs[i].label == tvt_set
]
tvt_set_start = tvt_set_indexes[0]
tvt_set_end = tvt_set_indexes[-1] + 1
tfr_i = 0
tfr_start = tvt_set_start
tfr_end = min(tfr_start + options.seqs_per_tfr, tvt_set_end)
while tfr_start <= tvt_set_end:
tfr_stem = '%s/%s-%d' % (tfr_dir, tvt_set, tfr_i)
cmd = 'basenji_data_write.py'
cmd += ' -s %d' % tfr_start
cmd += ' -e %d' % tfr_end
# do not use
# if options.umap_bed is not None:
# cmd += ' -u %s' % unmap_npy
# if options.umap_set is not None:
# cmd += ' --umap_set %f' % options.umap_set
cmd += ' %s' % fasta_file
cmd += ' %s' % seqs_bed_file
cmd += ' %s' % seqs_cov_dir
cmd += ' %s.tfr' % tfr_stem
if options.run_local:
# breaks on some OS
# cmd += ' &> %s.err' % tfr_stem
write_jobs.append(cmd)
else:
j = slurm.Job(cmd,
name='write_%s-%d' % (tvt_set, tfr_i),
out_file='%s.out' % tfr_stem,
err_file='%s.err' % tfr_stem,
queue='standard',
mem=15000,
time='12:0:0')
write_jobs.append(j)
# update
tfr_i += 1
tfr_start += options.seqs_per_tfr
tfr_end = min(tfr_start + options.seqs_per_tfr, tvt_set_end)
if options.run_local:
util.exec_par(write_jobs, options.processes, verbose=True)
else:
slurm.multi_run(write_jobs,
options.processes,
verbose=True,
launch_sleep=1,
update_sleep=5)
################################################################
# stats
################################################################
stats_dict = {}
stats_dict['num_targets'] = targets_df.shape[0]
stats_dict['train_seqs'] = len(train_mseqs)
stats_dict['valid_seqs'] = len(valid_mseqs)
stats_dict['test_seqs'] = len(test_mseqs)
stats_dict['seq_length'] = options.seq_length
stats_dict['pool_width'] = options.pool_width
stats_dict['crop_bp'] = options.crop_bp
stats_dict['diagonal_offset'] = options.diagonal_offset
target1_length = options.seq_length - 2 * options.crop_bp
target1_length = target1_length // options.pool_width
target1_length = target1_length - options.diagonal_offset
target_length = target1_length * (target1_length + 1) // 2
stats_dict['target_length'] = target_length
with open('%s/statistics.json' % options.out_dir, 'w') as stats_json_out:
json.dump(stats_dict, stats_json_out, indent=4)
def main():
usage = 'usage: %prog [options] <fasta_file> <sample_wigs_file> <hdf5_file>'
parser = OptionParser(usage)
parser.add_option(
'-b',
dest='limit_bed',
help='Limit to segments that overlap regions in a BED file')
parser.add_option(
'-c',
dest='clip',
default=None,
type='float',
help='Clip target values to have minimum [Default: %default]')
parser.add_option('--cluster_dir',
dest='cluster_dir',
default='basenji_hdf5')
parser.add_option('-d',
dest='sample_pct',
default=1.0,
type='float',
help='Down-sample the segments')
parser.add_option('-f',
dest='fourier_dim',
default=None,
type='int',
help='Fourier transform dimension [Default: %default]')
parser.add_option('-g',
dest='gaps_file',
help='Genome assembly gaps BED [Default: %default]')
parser.add_option('-l',
dest='seq_length',
default=1024,
type='int',
help='Sequence length [Default: %default]')
parser.add_option(
'--log2',
dest='log10to2',
default=False,
action='store_true',
help='Transform values from log10 to log2 [Default: %default]')
parser.add_option(
'--mult_cov',
dest='cov_multiplier',
default=1,
type='float',
help=
'Coverage multiplier, useful when the read extension and pool width do not match [Default: %default]'
)
parser.add_option(
'-n',
dest='na_t',
default=0.25,
type='float',
help=
'Remove sequences with an NA% greater than this threshold [Default: %default]'
)
parser.add_option(
'-o',
dest='out_bed_file',
help='Output the train/valid/test sequences as a BED file')
parser.add_option(
'-p',
dest='processes',
default=1,
type='int',
help='Number parallel processes to load data [Default: %default]')
parser.add_option('-s',
dest='stride',
type='int',
help='Stride to advance segments [Default: seq_length]')
parser.add_option(
'-t',
dest='test_pct_or_chr',
type='str',
default=0.05,
help='Proportion of the data for testing [Default: %default]')
parser.add_option('-u',
dest='unmap_bed',
help='Unmappable segments to set to NA')
parser.add_option('-w',
dest='pool_width',
type='int',
default=1,
help='Average pooling width [Default: %default]')
parser.add_option(
'-v',
dest='valid_pct_or_chr',
type='str',
default=0.05,
help='Proportion of the data for validation [Default: %default]')
parser.add_option('-z',
dest='compression',
help='h5py compression [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 3:
parser.error(
'Must provide genome FASTA file, sample Wig/BigWig labels and paths, '
'and model output file')
else:
fasta_file = args[0]
sample_wigs_file = args[1]
hdf5_file = args[2]
random.seed(1)
if options.stride is None:
options.stride = options.seq_length
################################################################
# assess bigwigs
################################################################
# get wig files and labels
target_wigs = OrderedDict()
target_strands = []
target_labels = []
for line in open(sample_wigs_file, encoding='UTF-8'):
a = line.rstrip().split('\t')
if a[0] in target_wigs:
print('WARNING: duplicate target id %s' % a[0], file=sys.stderr)
target_wigs[a[0]] = a[1]
target_strands.append(a[2])
if len(a) > 3:
target_labels.append(a[3])
else:
target_labels.append('')
if options.fourier_dim is not None and 2 * options.fourier_dim >= options.seq_length / options.pool_width:
print(
"Fourier transform to %d dims won't compress %d length sequences with %d pooling"
% (options.fourier_dim, options.seq_length, options.pool_width),
file=sys.stderr)
exit(1)
################################################################
# prepare genomic segments
################################################################
chrom_segments = genome.load_chromosomes(fasta_file)
# remove gaps
if options.gaps_file:
chrom_segments = genome.split_contigs(chrom_segments,
options.gaps_file)
# ditch the chromosomes
segments = []
for chrom in chrom_segments:
segments += [(chrom, seg_start, seg_end)
for seg_start, seg_end in chrom_segments[chrom]]
# standardize order
segments.sort()
# filter for large enough
segments = [
cse for cse in segments if cse[2] - cse[1] >= options.seq_length
]
# down-sample
if options.sample_pct < 1.0:
segments = random.sample(segments,
int(options.sample_pct * len(segments)))
# limit to a BED file
if options.limit_bed is not None:
segments = limit_segments(segments, options.limit_bed)
if not os.path.isdir(options.cluster_dir):
os.mkdir(options.cluster_dir)
# print segments to BED file
seg_bed_file = '%s/segments.bed' % options.cluster_dir
seg_bed_out = open(seg_bed_file, 'w')
for chrom, seg_start, seg_end in segments:
print('%s\t%d\t%d' % (chrom, seg_start, seg_end), file=seg_bed_out)
seg_bed_out.close()
################################################################
# bigwig read and process
################################################################
print('Reading and pre-processing bigwigs for %d segments' % len(segments),
flush=True)
targets_real = []
targets_imag = []
# generate numpy arrays on cluster
jobs = []
for target_label in target_wigs.keys():
wig_file = target_wigs[target_label]
npy_file = '%s/%s' % (options.cluster_dir, target_label)
if not os.path.isfile(npy_file) and not os.path.isfile(
'%s.npy' % npy_file):
print(npy_file)
if os.path.splitext(wig_file)[1] == '.h5':
script = 'seqs_hdf5.py'
else:
script = 'bigwig_hdf5.py'
cmd = 'echo $HOSTNAME; %s -l %d -s %d -w %d %s %s %s' % (
script, options.seq_length, options.stride, options.pool_width,
wig_file, seg_bed_file, npy_file)
name = 'hdf5_%s' % target_label
outf = '%s/%s.out' % (options.cluster_dir, target_label)
errf = '%s/%s.err' % (options.cluster_dir, target_label)
j = slurm.Job(cmd,
name,
outf,
errf,
queue='standard,tbdisk',
mem=15000,
time='12:0:0')
jobs.append(j)
slurm.multi_run(jobs)
# load into targets_real, targets_imag
for target_label in target_wigs.keys():
npy_file = '%s/%s.npy' % (options.cluster_dir, target_label)
wig_targets = np.load(npy_file)
targets_real.append(wig_targets)
# transpose from TxSxL to SxLxT
targets_real = np.transpose(np.array(targets_real), axes=(1, 2, 0))
print('%d target sequences' % targets_real.shape[0])
################################################################
# one hot code sequences
################################################################
seqs_1hot, seqs_segments = segments_1hot(fasta_file, segments,
options.seq_length,
options.stride)
print('%d sequences one hot coded' % seqs_1hot.shape[0])
################################################################
# correct for unmappable regions
################################################################
if options.unmap_bed is not None:
seqs_na = annotate_na(seqs_segments, options.unmap_bed,
options.seq_length, options.pool_width)
# determine mappable sequences and update test indexes
map_indexes = []
for i in range(seqs_na.shape[0]):
# mappable
if seqs_na[i, :].mean(dtype='float64') < options.na_t:
map_indexes.append(i)
# unmappable
else:
# forget it
pass
# update data structures
targets_real = targets_real[map_indexes]
if options.fourier_dim is not None:
targets_imag = targets_imag[map_indexes]
seqs_1hot = seqs_1hot[map_indexes]
seqs_segments = [seqs_segments[mi] for mi in map_indexes]
seqs_na = seqs_na[map_indexes]
################################################################
# write to train, valid, test HDF5
################################################################
# choose test indexes
if options.test_pct_or_chr.startswith('chr'):
test_indexes = [
si for si in range(len(seqs_segments))
if seqs_segments[si][0] == options.test_pct_or_chr
]
else:
test_pct = float(options.test_pct_or_chr)
test_indexes = [
twi for twi in range(len(seqs_segments))
if random.random() < test_pct
]
# choose valid indexes
if options.valid_pct_or_chr.startswith('chr'):
# valid_indexes = np.array([seq_seg[0] == options.valid_pct_or_chr for seq_seg in seqs_segments])
valid_indexes = [
si for si in range(len(seqs_segments))
if seqs_segments[si][0] == options.valid_pct_or_chr
]
else:
valid_pct = float(options.valid_pct_or_chr)
valid_n = int(valid_pct * len(seqs_segments))
nontest_indexes = set(range(len(seqs_segments))) - set(test_indexes)
valid_indexes = random.sample(nontest_indexes, valid_n)
# remainder is training
train_indexes = list(
set(range(len(seqs_segments))) - set(valid_indexes) -
set(test_indexes))
# training may require shuffling
random.shuffle(train_indexes)
random.shuffle(valid_indexes)
random.shuffle(test_indexes)
# write to HDF5
hdf5_out = h5py.File(hdf5_file, 'w')
# store pooling
hdf5_out.create_dataset('pool_width', data=options.pool_width, dtype='int')
# store targets
target_ids = np.array(list(target_wigs.keys()), dtype='S')
hdf5_out.create_dataset('target_ids', data=target_ids)
target_labels = np.array(target_labels, dtype='S')
hdf5_out.create_dataset('target_labels', data=target_labels)
target_strands = np.array(target_strands, dtype='S')
hdf5_out.create_dataset('target_strands', data=target_strands)
# HDF5 train
hdf5_out.create_dataset('train_in',
data=seqs_1hot[train_indexes],
dtype='bool',
compression=options.compression)
hdf5_out.create_dataset('train_out',
data=targets_real[train_indexes],
dtype='float16',
compression=options.compression)
if options.fourier_dim is not None:
hdf5_out.create_dataset('train_out_imag',
data=targets_imag[train_indexes],
dtype='float16',
compression=options.compression)
hdf5_out.create_dataset('train_na',
data=seqs_na[train_indexes],
dtype='bool',
compression=options.compression)
# HDF5 valid
hdf5_out.create_dataset('valid_in',
data=seqs_1hot[valid_indexes],
dtype='bool',
compression=options.compression)
hdf5_out.create_dataset('valid_out',
data=targets_real[valid_indexes],
dtype='float16',
compression=options.compression)
if options.fourier_dim is not None:
hdf5_out.create_dataset('valid_out_imag',
data=targets_imag[valid_indexes],
dtype='float16',
compression=options.compression)
hdf5_out.create_dataset('valid_na',
data=seqs_na[valid_indexes],
dtype='bool',
compression=options.compression)
# HDF5 test
hdf5_out.create_dataset('test_in',
data=seqs_1hot[test_indexes],
dtype='bool',
compression=options.compression)
hdf5_out.create_dataset('test_out',
data=targets_real[test_indexes],
dtype='float16',
compression=options.compression)
if options.fourier_dim is not None:
hdf5_out.create_dataset('test_out_imag',
data=targets_imag[test_indexes],
dtype='float16',
compression=options.compression)
hdf5_out.create_dataset('test_na',
data=seqs_na[test_indexes],
dtype='bool',
compression=options.compression)
hdf5_out.close()
# output BED file
if options.out_bed_file:
out_bed_out = open(options.out_bed_file, 'w')
for si in train_indexes:
print('%s\t%d\t%d\ttrain' % seqs_segments[si], file=out_bed_out)
for si in valid_indexes:
print('%s\t%d\t%d\tvalid' % seqs_segments[si], file=out_bed_out)
for si in test_indexes:
print('%s\t%d\t%d\ttest' % seqs_segments[si], file=out_bed_out)
out_bed_out.close()
def main():
usage = "usage: %prog [options] <params_file> <model_file> <vcf_file>"
parser = OptionParser(usage)
parser.add_option(
"-b",
dest="batch_size",
default=256,
type="int",
help="Batch size [Default: %default]",
)
parser.add_option(
"-c",
dest="csv",
default=False,
action="store_true",
help="Print table as CSV [Default: %default]",
)
parser.add_option(
"-f",
dest="genome_fasta",
default="%s/data/hg19.fa" % os.environ["BASENJIDIR"],
help="Genome FASTA for sequences [Default: %default]",
)
parser.add_option(
"-g",
dest="genome_file",
default="%s/data/human.hg19.genome" % os.environ["BASENJIDIR"],
help="Chromosome lengths file [Default: %default]",
)
parser.add_option(
"--h5",
dest="out_h5",
default=False,
action="store_true",
help="Output stats to sad.h5 [Default: %default]",
)
parser.add_option(
"--local",
dest="local",
default=1024,
type="int",
help="Local SAD score [Default: %default]",
)
parser.add_option("-n",
dest="norm_file",
default=None,
help="Normalize SAD scores")
parser.add_option(
"-o",
dest="out_dir",
default="sad",
help="Output directory for tables and plots [Default: %default]",
)
parser.add_option(
"-p",
dest="processes",
default=None,
type="int",
help="Number of processes, passed by multi script",
)
parser.add_option(
"--pseudo",
dest="log_pseudo",
default=1,
type="float",
help="Log2 pseudocount [Default: %default]",
)
parser.add_option(
"-q",
dest="queue",
default="k80",
help="SLURM queue on which to run the jobs [Default: %default]",
)
parser.add_option(
"-r",
dest="restart",
default=False,
action="store_true",
help="Restart a partially completed job [Default: %default]",
)
parser.add_option(
"--rc",
dest="rc",
default=False,
action="store_true",
help=
"Average forward and reverse complement predictions [Default: %default]",
)
parser.add_option(
"--shifts",
dest="shifts",
default="0",
type="str",
help="Ensemble prediction shifts [Default: %default]",
)
parser.add_option(
"--stats",
dest="sad_stats",
default="SAD,xSAR",
help="Comma-separated list of stats to save. [Default: %default]",
)
parser.add_option(
"-t",
dest="targets_file",
default=None,
type="str",
help="File specifying target indexes and labels in table format",
)
parser.add_option(
"--ti",
dest="track_indexes",
default=None,
type="str",
help="Comma-separated list of target indexes to output BigWig tracks",
)
parser.add_option(
"-u",
dest="penultimate",
default=False,
action="store_true",
help="Compute SED in the penultimate layer [Default: %default]",
)
parser.add_option(
"-z",
dest="out_zarr",
default=False,
action="store_true",
help="Output stats to sad.zarr [Default: %default]",
)
(options, args) = parser.parse_args()
if len(args) != 3:
parser.error("Must provide parameters and model files and VCF file")
else:
params_file = args[0]
model_file = args[1]
vcf_file = args[2]
#######################################################
# prep work
# output directory
if not options.restart:
if os.path.isdir(options.out_dir):
print("Please remove %s" % options.out_dir, file=sys.stderr)
exit(1)
os.mkdir(options.out_dir)
# pickle options
options_pkl_file = "%s/options.pkl" % options.out_dir
options_pkl = open(options_pkl_file, "wb")
pickle.dump(options, options_pkl)
options_pkl.close()
#######################################################
# launch worker threads
jobs = []
for pi in range(options.processes):
if not options.restart or not job_completed(options, pi):
cmd = "source activate tf1.12-gpu; basenji_sadf.py %s %s %d" % (
options_pkl_file,
" ".join(args),
pi,
)
name = "sad_p%d" % pi
outf = "%s/job%d.out" % (options.out_dir, pi)
errf = "%s/job%d.err" % (options.out_dir, pi)
j = slurm.Job(
cmd,
name,
outf,
errf,
queue=options.queue,
gpu=1,
mem=15000,
time="7-0:0:0",
)
jobs.append(j)
slurm.multi_run(jobs,
max_proc=options.processes,
verbose=True,
launch_sleep=10,
update_sleep=60)
#######################################################
# collect output
if options.out_h5:
collect_h5("sad.h5", options.out_dir, options.processes)
elif options.out_zarr:
collect_zarr("sad.zarr", options.out_dir, options.processes)
else:
collect_table("sad_table.txt", options.out_dir, options.processes)
def main():
usage = 'usage: %prog [options] <exp_dir> <params_file> <data_dir> <bed_file>'
parser = OptionParser(usage)
# sat options
sat_options = OptionGroup(parser, 'basenji_sat_bed.py options')
sat_options.add_option(
'-d',
dest='mut_down',
default=0,
type='int',
help=
'Nucleotides downstream of center sequence to mutate [Default: %default]'
)
sat_options.add_option(
'-f',
dest='genome_fasta',
default=None,
help='Genome FASTA for sequences [Default: %default]')
sat_options.add_option(
'-l',
dest='mut_len',
default=0,
type='int',
help='Length of center sequence to mutate [Default: %default]')
sat_options.add_option('-o',
dest='out_dir',
default='sat_mut',
help='Output directory [Default: %default]')
sat_options.add_option('--plots',
dest='plots',
default=False,
action='store_true',
help='Make heatmap plots [Default: %default]')
sat_options.add_option('-p',
dest='processes',
default=None,
type='int',
help='Number of processes, passed by multi script')
sat_options.add_option(
'--rc',
dest='rc',
default=False,
action='store_true',
help=
'Ensemble forward and reverse complement predictions [Default: %default]'
)
sat_options.add_option(
'--shifts',
dest='shifts',
default='0',
help='Ensemble prediction shifts [Default: %default]')
sat_options.add_option(
'--stats',
dest='sad_stats',
default='sum',
help='Comma-separated list of stats to save. [Default: %default]')
sat_options.add_option(
'-t',
dest='targets_file',
default=None,
type='str',
help='File specifying target indexes and labels in table format')
sat_options.add_option(
'-u',
dest='mut_up',
default=0,
type='int',
help=
'Nucleotides upstream of center sequence to mutate [Default: %default]'
)
parser.add_option_group(sat_options)
phylop_options = OptionGroup(parser, 'basenji_bench_phylop.py options')
# phylop_options.add_option('-e', dest='num_estimators',
# default=100, type='int',
# help='Number of random forest estimators [Default: %default]')
phylop_options.add_option(
'-g',
dest='genome',
default='ce11',
help='PhyloP and FASTA genome [Default: %default]')
# phylop_options.add_option('--pca', dest='n_components',
# default=None, type='int',
# help='PCA n_components [Default: %default]')
parser.add_option_group(phylop_options)
fold_options = OptionGroup(parser, 'cross-fold options')
fold_options.add_option(
'-a',
'--alt',
dest='alternative',
default='two-sided',
help='Statistical test alternative [Default: %default]')
fold_options.add_option(
'-c',
dest='crosses',
default=1,
type='int',
help='Number of cross-fold rounds [Default:%default]')
fold_options.add_option('-e',
dest='conda_env',
default='tf2-gpu',
help='Anaconda environment [Default: %default]')
fold_options.add_option('--label_exp',
dest='label_exp',
default='Experiment',
help='Experiment label [Default: %default]')
fold_options.add_option('--label_ref',
dest='label_ref',
default='Reference',
help='Reference label [Default: %default]')
fold_options.add_option('--name',
dest='name',
default='sat',
help='SLURM name prefix [Default: %default]')
fold_options.add_option(
'-q',
dest='queue',
default='gtx1080ti',
help='SLURM queue on which to run the jobs [Default: %default]')
fold_options.add_option('-r',
dest='ref_dir',
default=None,
help='Reference directory for statistical tests')
parser.add_option_group(fold_options)
(options, args) = parser.parse_args()
if len(args) != 4:
parser.error('Must provide parameters file and data directory')
else:
exp_dir = args[0]
params_file = args[1]
data_dir = args[2]
bed_file = args[3]
# read data parameters
data_stats_file = '%s/statistics.json' % data_dir
with open(data_stats_file) as data_stats_open:
data_stats = json.load(data_stats_open)
# count folds
num_folds = len([dkey for dkey in data_stats if dkey.startswith('fold')])
# genome
genome_path = os.environ[options.genome.upper()]
options.genome_fasta = '%s/assembly/%s.fa' % (genome_path, options.genome)
################################################################
# saturation mutagenesis
################################################################
jobs = []
scores_files = []
for ci in range(options.crosses):
for fi in range(num_folds):
it_dir = '%s/f%d_c%d' % (exp_dir, fi, ci)
# update output directory
sat_dir = '%s/%s' % (it_dir, options.out_dir)
# check if done
scores_file = '%s/scores.h5' % sat_dir
scores_files.append(scores_file)
if os.path.isfile(scores_file):
print('%s already generated.' % scores_file)
else:
basenji_cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
basenji_cmd += ' conda activate %s;' % options.conda_env
basenji_cmd += ' echo $HOSTNAME;'
basenji_cmd += ' basenji_sat_bed.py'
basenji_cmd += ' %s' % options_string(options, sat_options,
sat_dir)
basenji_cmd += ' %s' % params_file
basenji_cmd += ' %s/train/model_best.h5' % it_dir
basenji_cmd += ' %s' % bed_file
name = '%s-f%dc%d' % (options.name, fi, ci)
basenji_job = slurm.Job(basenji_cmd,
name,
out_file='%s.out' % sat_dir,
err_file='%s.err' % sat_dir,
cpu=2,
gpu=1,
queue=options.queue,
mem=30000,
time='7-0:00:00')
jobs.append(basenji_job)
slurm.multi_run(jobs, verbose=True)
################################################################
# ensemble
################################################################
ensemble_dir = '%s/ensemble' % exp_dir
if not os.path.isdir(ensemble_dir):
os.mkdir(ensemble_dir)
sat_dir = '%s/%s' % (ensemble_dir, options.out_dir)
if not os.path.isdir(sat_dir):
os.mkdir(sat_dir)
if not os.path.isfile('%s/scores.h5' % sat_dir):
print('Generating ensemble scores.')
ensemble_scores_h5(sat_dir, scores_files)
else:
print('Ensemble scores already generated.')
################################################################
# PhyloP regressors
################################################################
# num_pcs = int(data_stats['num_targets']**0.75)
jobs = []
for ci in range(options.crosses):
for fi in range(num_folds):
it_dir = '%s/f%d_c%d' % (exp_dir, fi, ci)
sat_dir = '%s/%s' % (it_dir, options.out_dir)
if not os.path.isfile('%s/stats.txt' % sat_dir):
phylop_cmd = 'basenji_bench_phylop.py'
phylop_cmd += ' -e 200 -p 4'
# phylop_cmd += ' -d %d' % num_pcs
phylop_cmd += ' -o %s' % sat_dir
phylop_cmd += ' %s/scores.h5' % sat_dir
name = '%s-f%dc%d' % (options.name, fi, ci)
std_pre = '%s/phylop' % sat_dir
j = slurm.Job(phylop_cmd,
name,
'%s.out' % std_pre,
'%s.err' % std_pre,
queue='standard',
cpu=4,
mem=45000,
time='1-0:0:0')
jobs.append(j)
# ensemble
sat_dir = '%s/%s' % (ensemble_dir, options.out_dir)
if not os.path.isfile('%s/stats.txt' % sat_dir):
phylop_cmd = 'basenji_bench_phylop.py'
phylop_cmd += ' -e 200 -p 4'
# phylop_cmd += ' -d %d' % num_pcs
phylop_cmd += ' -o %s' % sat_dir
phylop_cmd += ' %s/scores.h5' % sat_dir
name = '%s-ens' % options.name
std_pre = '%s/phylop' % sat_dir
j = slurm.Job(phylop_cmd,
name,
'%s.out' % std_pre,
'%s.err' % std_pre,
queue='standard',
cpu=4,
mem=45000,
time='1-0:0:0')
jobs.append(j)
slurm.multi_run(jobs, verbose=True)
################################################################
# compare
################################################################
ref_sat_dirs = []
exp_sat_dirs = []
for ci in range(options.crosses):
for fi in range(num_folds):
exp_sat_dir = '%s/f%d_c%d/%s' % (exp_dir, fi, ci, options.out_dir)
exp_sat_dirs.append(exp_sat_dir)
if options.ref_dir is not None:
ref_sat_dir = '%s/f%d_c%d/%s' % (options.ref_dir, fi, ci,
options.out_dir)
ref_sat_dirs.append(ref_sat_dir)
exp_pcor_folds, exp_r2_folds = read_metrics(exp_sat_dirs)
exp_sat_dirs = ['%s/ensemble/%s' % (exp_dir, options.out_dir)]
exp_pcor_ens, exp_r2_ens = read_metrics(exp_sat_dirs)
if options.ref_dir is not None:
ref_pcor_folds, ref_r2_folds = read_metrics(ref_sat_dirs)
ref_sat_dirs = ['%s/ensemble/%s' % (options.ref_dir, options.out_dir)]
ref_pcor_ens, ref_r2_ens = read_metrics(ref_sat_dirs)
print('PearsonR')
exp_mean = exp_pcor_folds.mean()
exp_stdm = exp_pcor_folds.std() / np.sqrt(len(exp_pcor_folds))
expe_mean = exp_pcor_ens.mean()
expe_stdm = exp_pcor_ens.std() / np.sqrt(len(exp_pcor_ens))
print('%12s: %.4f (%.4f)' % (options.label_exp, exp_mean, exp_stdm))
print('%12s (ens): %.4f (%.4f)' %
(options.label_exp, expe_mean, expe_stdm))
if options.ref_dir is not None:
ref_mean = ref_pcor_folds.mean()
ref_stdm = ref_pcor_folds.std() / np.sqrt(len(ref_pcor_folds))
refe_mean = ref_pcor_ens.mean()
refe_stdm = ref_pcor_ens.std() / np.sqrt(len(ref_pcor_ens))
print('%12s: %.4f (%.4f)' %
(options.label_ref, ref_mean, ref_stdm))
print('%12s (ens): %.4f (%.4f)' %
(options.label_ref, refe_mean, refe_stdm))
mwp, tp = stat_tests(exp_pcor_folds, ref_pcor_folds,
options.alternative)
print('Mann-Whitney U p-value: %.3g' % mwp)
print('T-test p-value: %.3g' % tp)
print('\nR2')
exp_mean = exp_r2_folds.mean()
exp_stdm = exp_r2_folds.std() / np.sqrt(len(exp_r2_folds))
expe_mean = exp_r2_ens.mean()
expe_stdm = exp_r2_ens.std() / np.sqrt(len(exp_r2_ens))
print('%12s: %.4f (%.4f)' % (options.label_exp, exp_mean, exp_stdm))
print('%12s (ens): %.4f (%.4f)' %
(options.label_exp, expe_mean, expe_stdm))
if options.ref_dir is not None:
ref_mean = ref_r2_folds.mean()
ref_stdm = ref_r2_folds.std() / np.sqrt(len(ref_r2_folds))
refe_mean = ref_r2_ens.mean()
refe_stdm = ref_r2_ens.std() / np.sqrt(len(ref_r2_ens))
print('%12s: %.4f (%.4f)' %
(options.label_ref, ref_mean, ref_stdm))
print('%12s (ens): %.4f (%.4f)' %
(options.label_ref, refe_mean, refe_stdm))
mwp, tp = stat_tests(exp_r2_folds, ref_r2_folds, options.alternative)
print('Mann-Whitney U p-value: %.3g' % mwp)
print('T-test p-value: %.3g' % tp)
def main():
usage = 'usage: %prog [options] <params_file> <model_file> <vcf_file>'
parser = OptionParser(usage)
# scd
parser.add_option('-f', dest='genome_fasta',
default='%s/data/hg19.fa' % os.environ['BASENJIDIR'],
help='Genome FASTA for sequences [Default: %default]')
parser.add_option('-m', dest='plot_map',
default=False, action='store_true',
help='Plot contact map for each allele [Default: %default]')
parser.add_option('-o',dest='out_dir',
default='scd',
help='Output directory for tables and plots [Default: %default]')
parser.add_option('--rc', dest='rc',
default=False, action='store_true',
help='Average forward and reverse complement predictions [Default: %default]')
parser.add_option('--shifts', dest='shifts',
default='0', type='str',
help='Ensemble prediction shifts [Default: %default]')
parser.add_option('--stats', dest='scd_stats',
default='SCD',
help='Comma-separated list of stats to save. [Default: %default]')
parser.add_option('-t', dest='targets_file',
default=None, type='str',
help='File specifying target indexes and labels in table format')
# multi
parser.add_option('--cpu', dest='cpu',
default=False, action='store_true',
help='Run without a GPU [Default: %default]')
parser.add_option('--name', dest='name',
default='scd', help='SLURM name prefix [Default: %default]')
parser.add_option('--max_proc', dest='max_proc',
default=None, type='int',
help='Maximum concurrent processes [Default: %default]')
parser.add_option('-p', dest='processes',
default=None, type='int',
help='Number of processes, passed by multi script')
parser.add_option('-q', dest='queue',
default='gtx1080ti',
help='SLURM queue on which to run the jobs [Default: %default]')
parser.add_option('-r', dest='restart',
default=False, action='store_true',
help='Restart a partially completed job [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 3:
parser.error('Must provide parameters and model files and VCF file')
else:
params_file = args[0]
model_file = args[1]
vcf_file = args[2]
#######################################################
# prep work
# output directory
if not options.restart:
if os.path.isdir(options.out_dir):
print('Please remove %s' % options.out_dir, file=sys.stderr)
exit(1)
os.mkdir(options.out_dir)
# pickle options
options_pkl_file = '%s/options.pkl' % options.out_dir
options_pkl = open(options_pkl_file, 'wb')
pickle.dump(options, options_pkl)
options_pkl.close()
#######################################################
# launch worker threads
jobs = []
for pi in range(options.processes):
if not options.restart or not job_completed(options, pi):
if options.cpu:
cmd = ''
else:
cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
cmd += 'conda activate tf1.15-gpu;'
cmd += ' akita_scd.py %s %s %d' % (
options_pkl_file, ' '.join(args), pi)
name = '%s_p%d' % (options.name, pi)
outf = '%s/job%d.out' % (options.out_dir, pi)
errf = '%s/job%d.err' % (options.out_dir, pi)
num_gpu = 1*(not options.cpu)
j = slurm.Job(cmd, name,
outf, errf,
queue=options.queue, gpu=num_gpu,
mem=15000, time='14-0:0:0')
jobs.append(j)
slurm.multi_run(jobs, max_proc=options.max_proc, verbose=True,
launch_sleep=10, update_sleep=60)
#######################################################
# collect output
collect_h5('scd.h5', options.out_dir, options.processes)
def main():
usage = 'usage: %prog [options] <exp_dir> <params_file> <data_dir>'
parser = OptionParser(usage)
parser.add_option('-a',
'--alt',
dest='alternative',
default='two-sided',
help='Statistical test alternative [Default: %default]')
parser.add_option('-d',
dest='dataset_i',
default=None,
type='int',
help='Dataset index [Default:%default]')
parser.add_option('-e',
dest='conda_env',
default='tf2-gpu',
help='Anaconda environment [Default: %default]')
parser.add_option('--name',
dest='name',
default='test',
help='SLURM name prefix [Default: %default]')
parser.add_option('-q', dest='queue', default='gtx1080ti')
parser.add_option('-r',
dest='ref_dir',
default=None,
help='Reference directory for statistical tests')
parser.add_option(
'--rc',
dest='rc',
default=False,
action='store_true',
help=
'Average forward and reverse complement predictions [Default: %default]'
)
parser.add_option('--shifts',
dest='shifts',
default='0',
type='str',
help='Ensemble prediction shifts [Default: %default]')
parser.add_option('--spec',
dest='specificity',
default=False,
action='store_true',
help='Test specificity [Default: %default]')
parser.add_option('--train',
dest='train',
default=False,
action='store_true',
help='Test on the training set, too [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 3:
parser.error('Must provide parameters file and data directory')
else:
exp_dir = args[0]
params_file = args[1]
data_dirs = [os.path.abspath(arg) for arg in args[2:]]
if options.dataset_i is None:
head_i = 0
else:
head_i = options.dataset_i
iterations = len(glob.glob('%s/*' % exp_dir))
################################################################
# test check
################################################################
jobs = []
if options.train:
for i in range(iterations):
it_dir = '%s/%d' % (exp_dir, i)
if options.dataset_i is None:
out_dir = '%s/test_train' % it_dir
model_file = '%s/train/model_check.h5' % it_dir
data_dir = data_dirs[0]
else:
out_dir = '%s/test%d_train' % (it_dir, options.dataset_i)
model_file = '%s/train/model%d_check.h5' % (it_dir,
options.dataset_i)
data_dir = data_dirs[options.dataset_i]
# check if done
acc_file = '%s/acc.txt' % out_dir
if os.path.isfile(acc_file):
print('%s already generated.' % acc_file)
else:
cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
cmd += ' conda activate %s;' % options.conda_env
cmd += ' basenji_test.py'
cmd += ' --head %d' % head_i
cmd += ' -o %s' % out_dir
if options.rc:
cmd += ' --rc'
if options.shifts:
cmd += ' --shifts %s' % options.shifts
cmd += ' --split train'
cmd += ' %s' % params_file
cmd += ' %s' % model_file
cmd += ' %s' % data_dir
name = '%s-testtr%d' % (options.name, i)
j = slurm.Job(cmd,
name=name,
out_file='%s.out' % out_dir,
err_file='%s.err' % out_dir,
queue=options.queue,
cpu=1,
gpu=1,
mem=23000,
time='4:00:00')
jobs.append(j)
################################################################
# test best
################################################################
for i in range(iterations):
it_dir = '%s/%d' % (exp_dir, i)
if options.dataset_i is None:
out_dir = '%s/test' % it_dir
model_file = '%s/train/model_best.h5' % it_dir
data_dir = data_dirs[0]
else:
out_dir = '%s/test%d' % (it_dir, options.dataset_i)
model_file = '%s/train/model%d_best.h5' % (it_dir,
options.dataset_i)
data_dir = data_dirs[options.dataset_i]
# check if done
acc_file = '%s/acc.txt' % out_dir
if os.path.isfile(acc_file):
print('%s already generated.' % acc_file)
else:
# basenji test
cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
cmd += ' conda activate %s;' % options.conda_env
cmd += ' basenji_test.py'
cmd += ' --head %d' % head_i
cmd += ' -o %s' % out_dir
if options.rc:
cmd += ' --rc'
if options.shifts:
cmd += ' --shifts %s' % options.shifts
cmd += ' %s' % params_file
cmd += ' %s' % model_file
cmd += ' %s' % data_dir
name = '%s-test%d' % (options.name, i)
j = slurm.Job(cmd,
name=name,
out_file='%s.out' % out_dir,
err_file='%s.err' % out_dir,
queue=options.queue,
cpu=1,
gpu=1,
mem=23000,
time='4:00:00')
jobs.append(j)
################################################################
# test best specificity
################################################################
if options.specificity:
for i in range(iterations):
it_dir = '%s/%d' % (exp_dir, i)
if options.dataset_i is None:
out_dir = '%s/test_spec' % it_dir
model_file = '%s/train/model_best.h5' % it_dir
data_dir = data_dirs[0]
else:
out_dir = '%s/test%d_spec' % (it_dir, di)
model_file = '%s/train/model%d_best.h5' % (it_dir, di)
data_dir = data_dirs[options.dataset_i]
# check if done
acc_file = '%s/acc.txt' % out_dir
if os.path.isfile(acc_file):
print('%s already generated.' % acc_file)
else:
# basenji test
cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
cmd += ' conda activate %s;' % options.conda_env
cmd += ' basenji_test_specificity.py'
cmd += ' --head %d' % head_i
cmd += ' -o %s' % out_dir
if options.rc:
cmd += ' --rc'
if options.shifts:
cmd += ' --shifts %s' % options.shifts
cmd += ' %s' % params_file
cmd += ' %s' % model_file
cmd += ' %s' % data_dir
name = '%s-spec%d' % (options.name, i)
j = slurm.Job(cmd,
name=name,
out_file='%s.out' % out_dir,
err_file='%s.err' % out_dir,
queue=options.queue,
cpu=1,
gpu=1,
mem=75000,
time='6:00:00')
jobs.append(j)
slurm.multi_run(jobs, verbose=True)
if options.ref_dir is not None:
################################################################
# compare checkpoint on training set
################################################################
if options.train:
ref_glob_str = '%s/*/test_train/acc.txt' % options.ref_dir
ref_cors, ref_mean, ref_stdm = read_cors(ref_glob_str)
exp_glob_str = '%s/*/test_train/acc.txt' % exp_dir
exp_cors, exp_mean, exp_stdm = read_cors(exp_glob_str)
mwp, tp = stat_tests(ref_cors, exp_cors, options.alternative)
print('\nTrain:')
print('Reference PearsonR: %.4f (%.4f)' % (ref_mean, ref_stdm))
print('Experiment PearsonR: %.4f (%.4f)' % (exp_mean, exp_stdm))
print('Mann-Whitney U p-value: %.3g' % mwp)
print('T-test p-value: %.3g' % tp)
################################################################
# compare best on test set
################################################################
ref_glob_str = '%s/*/test/acc.txt' % options.ref_dir
ref_cors, ref_mean, ref_stdm = read_cors(ref_glob_str)
exp_glob_str = '%s/*/test/acc.txt' % exp_dir
exp_cors, exp_mean, exp_stdm = read_cors(exp_glob_str)
mwp, tp = stat_tests(ref_cors, exp_cors, options.alternative)
print('\nTest:')
print('Reference PearsonR: %.4f (%.4f)' % (ref_mean, ref_stdm))
print('Experiment PearsonR: %.4f (%.4f)' % (exp_mean, exp_stdm))
print('Mann-Whitney U p-value: %.3g' % mwp)
print('T-test p-value: %.3g' % tp)
################################################################
# compare best on test set specificity
################################################################
if options.specificity:
ref_glob_str = '%s/*/test_spec/acc.txt' % options.ref_dir
ref_cors, ref_mean, ref_stdm = read_cors(ref_glob_str)
exp_glob_str = '%s/*/test_spec/acc.txt' % exp_dir
exp_cors, exp_mean, exp_stdm = read_cors(exp_glob_str)
mwp, tp = stat_tests(ref_cors, exp_cors, options.alternative)
print('\nSpecificity:')
print('Reference PearsonR: %.4f (%.4f)' % (ref_mean, ref_stdm))
print('Experiment PearsonR: %.4f (%.4f)' % (exp_mean, exp_stdm))
print('Mann-Whitney U p-value: %.3g' % mwp)
print('T-test p-value: %.3g' % tp)
def main():
usage = 'usage: %prog [options] <model> <vcf_file>'
parser = OptionParser(usage)
# sad
parser.add_option('-b',
dest='batch_size',
default=4,
type='int',
help='Batch size [Default: %default]')
parser.add_option('-c',
dest='slice_center',
default=None,
type='int',
help='Slice center positions [Default: %default]')
parser.add_option('-f',
dest='genome_fasta',
default='%s/data/hg19.fa' % os.environ['BASENJIDIR'],
help='Genome FASTA for sequences [Default: %default]')
parser.add_option(
'-o',
dest='out_dir',
default='sad',
help='Output directory for tables and plots [Default: %default]')
parser.add_option('--pseudo',
dest='log_pseudo',
default=1,
type='float',
help='Log2 pseudocount [Default: %default]')
parser.add_option(
'--rc',
dest='rc',
default=False,
action='store_true',
help=
'Average forward and reverse complement predictions [Default: %default]'
)
parser.add_option('--shifts',
dest='shifts',
default='0',
type='str',
help='Ensemble prediction shifts [Default: %default]')
parser.add_option('--species', dest='species', default='human')
parser.add_option(
'--stats',
dest='sad_stats',
default='SAD',
help='Comma-separated list of stats to save. [Default: %default]')
parser.add_option(
'-t',
dest='targets_file',
default=None,
type='str',
help='File specifying target indexes and labels in table format')
# multi
parser.add_option('-e',
dest='conda_env',
default='tf2.2-gpu',
help='Anaconda environment [Default: %default]')
parser.add_option('--name',
dest='name',
default='sad',
help='SLURM name prefix [Default: %default]')
parser.add_option('--max_proc',
dest='max_proc',
default=None,
type='int',
help='Maximum concurrent processes [Default: %default]')
parser.add_option('-p',
dest='processes',
default=None,
type='int',
help='Number of processes, passed by multi script')
parser.add_option(
'-q',
dest='queue',
default='gtx1080ti',
help='SLURM queue on which to run the jobs [Default: %default]')
parser.add_option(
'-r',
dest='restart',
default=False,
action='store_true',
help='Restart a partially completed job [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 2:
parser.error('Must provide model and VCF file')
else:
model_file = args[0]
vcf_file = args[1]
#######################################################
# prep work
# output directory
if not options.restart:
if os.path.isdir(options.out_dir):
print('Please remove %s' % options.out_dir, file=sys.stderr)
exit(1)
os.mkdir(options.out_dir)
# pickle options
options_pkl_file = '%s/options.pkl' % options.out_dir
options_pkl = open(options_pkl_file, 'wb')
pickle.dump(options, options_pkl)
options_pkl.close()
#######################################################
# launch worker threads
jobs = []
for pi in range(options.processes):
if not options.restart or not job_completed(options, pi):
cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
cmd += ' conda activate %s;' % options.conda_env
cmd += ' sonnet_sad.py %s %s %d' % (options_pkl_file,
' '.join(args), pi)
name = '%s_p%d' % (options.name, pi)
outf = '%s/job%d.out' % (options.out_dir, pi)
errf = '%s/job%d.err' % (options.out_dir, pi)
j = slurm.Job(cmd,
name,
outf,
errf,
queue=options.queue,
gpu=1,
mem=22000,
time='14-0:0:0')
jobs.append(j)
slurm.multi_run(jobs,
max_proc=options.max_proc,
verbose=True,
launch_sleep=10,
update_sleep=60)
#######################################################
# collect output
collect_h5('sad.h5', options.out_dir, options.processes)
def main():
usage = ('usage: %prog [options] <params_file> <model_file> <genes_hdf5_file>'
' <vcf_file>')
parser = OptionParser(usage)
parser.add_option(
'-a',
dest='all_sed',
default=False,
action='store_true',
help=
'Print all variant-gene pairs, as opposed to only nonzero [Default: %default]'
)
parser.add_option(
'-b',
dest='batch_size',
default=None,
type='int',
help='Batch size [Default: %default]')
parser.add_option(
'-c',
dest='csv',
default=False,
action='store_true',
help='Print table as CSV [Default: %default]')
parser.add_option(
'-g',
dest='genome_file',
default='%s/data/human.hg19.genome' % os.environ['BASENJIDIR'],
help='Chromosome lengths file [Default: %default]')
parser.add_option(
'-o',
dest='out_dir',
default='sed',
help='Output directory for tables and plots [Default: %default]')
parser.add_option(
'-p',
dest='processes',
default=2,
type='int',
help='Number of parallel processes to run [Default: %default]')
parser.add_option(
'--pseudo',
dest='log_pseudo',
default=0.125,
type='float',
help='Log2 pseudocount [Default: %default]')
parser.add_option(
'-q',
dest='queue',
default='k80',
help='SLURM queue on which to run the jobs [Default: %default]')
parser.add_option(
'-r',
dest='tss_radius',
default=0,
type='int',
help='Radius of bins considered to quantify TSS transcription [Default: %default]')
parser.add_option(
'--rc',
dest='rc',
default=False,
action='store_true',
help=
'Average the forward and reverse complement predictions when testing [Default: %default]'
)
parser.add_option(
'--shifts',
dest='shifts',
default='0',
help='Ensemble prediction shifts [Default: %default]')
parser.add_option(
'-t',
dest='targets_file',
default=None,
help='File specifying target indexes and labels in table format.')
parser.add_option(
'--ti',
dest='track_indexes',
help='Comma-separated list of target indexes to output BigWig tracks')
parser.add_option(
'-u',
dest='penultimate',
default=False,
action='store_true',
help='Compute SED in the penultimate layer [Default: %default]')
parser.add_option(
'-x',
dest='tss_table',
default=False,
action='store_true',
help='Print TSS table in addition to gene [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 4:
parser.error(
'Must provide parameters and model files, genes HDF5 file, and QTL VCF'
' file')
else:
params_file = args[0]
model_file = args[1]
genes_hdf5_file = args[2]
vcf_file = args[3]
#######################################################
# prep work
# output directory
if os.path.isdir(options.out_dir):
shutil.rmtree(options.out_dir)
os.mkdir(options.out_dir)
# pickle options
options_pkl_file = '%s/options.pkl' % options.out_dir
options_pkl = open(options_pkl_file, 'wb')
pickle.dump(options, options_pkl)
options_pkl.close()
#######################################################
# launch worker threads
jobs = []
for pi in range(options.processes):
cmd = 'source activate py3_gpu; basenji_sed.py %s %s %d' % (
options_pkl_file, ' '.join(args), pi)
name = 'sed_p%d' % pi
outf = '%s/job%d.out' % (options.out_dir, pi)
errf = '%s/job%d.err' % (options.out_dir, pi)
j = slurm.Job(
cmd,
name,
outf,
errf,
queue=options.queue,
mem=30000,
time='4:0:0',
gpu=1)
jobs.append(j)
slurm.multi_run(jobs, max_proc=options.processes, verbose=True, sleep_time=60)
#######################################################
# collect output
collect_table_multi('sed_gene.txt', options.out_dir, options.processes, options.log_pseudo)
if options.tss_table:
collect_table('sed_tss.txt', options.out_dir, options.processes)
if options.track_indexes is not None:
if not os.path.isdir('%s/tracks' % options.out_dir):
os.mkdir('%s/tracks' % options.out_dir)
for track_file in glob.glob('%s/job*/tracks/*'):
track_base = os.path.split(track_file)[1]
os.rename(track_file, '%s/tracks/%s' % (options.out_dir, track_base))
for pi in range(options.processes):
shutil.rmtree('%s/job%d' % (options.out_dir, pi))
def main():
usage = "usage: %prog [options] <params_file> <model_file> <bed_file>"
parser = OptionParser(usage)
# basenji_sat_bed.py options
parser.add_option(
"-f",
dest="genome_fasta",
default=None,
help="Genome FASTA for sequences [Default: %default]",
)
parser.add_option(
"-l",
dest="mut_len",
default=200,
type="int",
help="Length of center sequence to mutate [Default: %default]",
)
parser.add_option(
"-o",
dest="out_dir",
default="sat_mut",
help="Output directory [Default: %default]",
)
parser.add_option(
"--plots",
dest="plots",
default=False,
action="store_true",
help="Make heatmap plots [Default: %default]",
)
parser.add_option(
"--rc",
dest="rc",
default=False,
action="store_true",
help=
"Ensemble forward and reverse complement predictions [Default: %default]",
)
parser.add_option(
"--shifts",
dest="shifts",
default="0",
help="Ensemble prediction shifts [Default: %default]",
)
parser.add_option(
"-t",
dest="targets_file",
default=None,
type="str",
help="File specifying target indexes and labels in table format",
)
# _multi.py options
parser.add_option(
"-n",
dest="name",
default="sat",
help="SLURM job name prefix [Default: %default]",
)
parser.add_option(
"-p",
dest="processes",
default=None,
type="int",
help="Number of processes, passed by multi script",
)
parser.add_option(
"-q",
dest="queue",
default="k80",
help="SLURM queue on which to run the jobs [Default: %default]",
)
parser.add_option(
"-r",
dest="restart",
default=False,
action="store_true",
help="Restart a partially completed job [Default: %default]",
)
(options, args) = parser.parse_args()
if len(args) != 3:
print(args)
parser.error("Must provide parameters and model files and BED file")
else:
params_file = args[0]
model_file = args[1]
bed_file = args[2]
#######################################################
# prep work
# output directory
if not options.restart:
if os.path.isdir(options.out_dir):
print("Please remove %s" % options.out_dir, file=sys.stderr)
exit(1)
os.mkdir(options.out_dir)
# pickle options
options_pkl_file = "%s/options.pkl" % options.out_dir
options_pkl = open(options_pkl_file, "wb")
pickle.dump(options, options_pkl)
options_pkl.close()
#######################################################
# launch worker threads
jobs = []
for pi in range(options.processes):
if not options.restart or not job_completed(options, pi):
cmd = "source activate tf1.12-gpu; basenji_sat_bed.py %s %s %d" % (
options_pkl_file,
" ".join(args),
pi,
)
name = "%s_p%d" % (options.name, pi)
outf = "%s/job%d.out" % (options.out_dir, pi)
errf = "%s/job%d.err" % (options.out_dir, pi)
j = slurm.Job(
cmd,
name,
outf,
errf,
queue=options.queue,
gpu=1,
mem=30000,
time="14-0:0:0",
)
jobs.append(j)
slurm.multi_run(jobs,
max_proc=options.processes,
verbose=True,
launch_sleep=10,
update_sleep=60)
#######################################################
# collect output
collect_h5(options.out_dir, options.processes)
def main():
usage = 'usage: %prog [options] <params_file> <model_file> <bed_file>'
parser = OptionParser(usage)
# basenji_sat_bed.py options
parser.add_option('-f',
dest='genome_fasta',
default='%s/assembly/hg19.fa' % os.environ['HG19'],
help='Genome FASTA for sequences [Default: %default]')
parser.add_option(
'-l',
dest='mut_len',
default=200,
type='int',
help='Length of center sequence to mutate [Default: %default]')
parser.add_option('-o',
dest='out_dir',
default='sat_mut',
help='Output directory [Default: %default]')
parser.add_option('--plots',
dest='plots',
default=False,
action='store_true',
help='Make heatmap plots [Default: %default]')
parser.add_option(
'--rc',
dest='rc',
default=False,
action='store_true',
help=
'Ensemble forward and reverse complement predictions [Default: %default]'
)
parser.add_option('--shifts',
dest='shifts',
default='0',
help='Ensemble prediction shifts [Default: %default]')
parser.add_option(
'-t',
dest='targets_file',
default=None,
type='str',
help='File specifying target indexes and labels in table format')
# _multi.py options
parser.add_option('-p',
dest='processes',
default=None,
type='int',
help='Number of processes, passed by multi script')
parser.add_option(
'-q',
dest='queue',
default='k80',
help='SLURM queue on which to run the jobs [Default: %default]')
parser.add_option(
'-r',
dest='restart',
default=False,
action='store_true',
help='Restart a partially completed job [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 3:
parser.error('Must provide parameters and model files and VCF file')
else:
params_file = args[0]
model_file = args[1]
bed_file = args[2]
#######################################################
# prep work
# output directory
if not options.restart:
if os.path.isdir(options.out_dir):
print('Please remove %s' % options.out_dir, file=sys.stderr)
exit(1)
os.mkdir(options.out_dir)
# pickle options
options_pkl_file = '%s/options.pkl' % options.out_dir
options_pkl = open(options_pkl_file, 'wb')
pickle.dump(options, options_pkl)
options_pkl.close()
#######################################################
# launch worker threads
jobs = []
for pi in range(options.processes):
if not options.restart or not job_completed(options, pi):
cmd = 'source activate py3_gpu; basenji_sat_bed.py %s %s %d' % (
options_pkl_file, ' '.join(args), pi)
name = 'sat_p%d' % pi
outf = '%s/job%d.out' % (options.out_dir, pi)
errf = '%s/job%d.err' % (options.out_dir, pi)
j = slurm.Job(cmd,
name,
outf,
errf,
queue=options.queue,
gpu=1,
mem=30000,
time='14-0:0:0')
jobs.append(j)
slurm.multi_run(jobs,
max_proc=options.processes,
verbose=True,
launch_sleep=10,
update_sleep=60)
#######################################################
# collect output
collect_h5(options.out_dir, options.processes)
def main():
usage = 'usage: %prog [options] <exp_dir> <params_file> <data_dir>'
parser = OptionParser(usage)
parser.add_option('-a',
'--alt',
dest='alternative',
default='two-sided',
help='Statistical test alternative [Default: %default]')
parser.add_option('-c',
dest='crosses',
default=1,
type='int',
help='Number of cross-fold rounds [Default:%default]')
parser.add_option('-e',
dest='conda_env',
default='tf2-gpu',
help='Anaconda environment [Default: %default]')
parser.add_option('--l1',
dest='label1',
default='Reference',
help='Reference label [Default: %default]')
parser.add_option('--l2',
dest='label2',
default='Experiment',
help='Experiment label [Default: %default]')
parser.add_option('--name',
dest='name',
default='test',
help='SLURM name prefix [Default: %default]')
parser.add_option('-o',
dest='out_stem',
default=None,
help='Outplut plot stem [Default: %default]')
parser.add_option('-q', dest='queue', default='gtx1080ti')
parser.add_option('-r',
dest='ref_dir',
default=None,
help='Reference directory for statistical tests')
parser.add_option(
'--rc',
dest='rc',
default=False,
action='store_true',
help=
'Average forward and reverse complement predictions [Default: %default]'
)
parser.add_option('--shifts',
dest='shifts',
default='0',
type='str',
help='Ensemble prediction shifts [Default: %default]')
parser.add_option('--spec',
dest='specificity',
default=False,
action='store_true',
help='Test specificity [Default: %default]')
parser.add_option('--train',
dest='train',
default=False,
action='store_true',
help='Test on the training set, too [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 3:
parser.error('Must provide parameters file and data directory')
else:
exp_dir = args[0]
params_file = args[1]
data_dir = args[2]
# read data parameters
data_stats_file = '%s/statistics.json' % data_dir
with open(data_stats_file) as data_stats_open:
data_stats = json.load(data_stats_open)
# count folds
num_folds = len([dkey for dkey in data_stats if dkey.startswith('fold')])
################################################################
# test check
################################################################
jobs = []
if options.train:
for ci in range(options.crosses):
for fi in range(num_folds):
it_dir = '%s/f%d_c%d' % (exp_dir, fi, ci)
# check if done
acc_file = '%s/test_train/acc.txt' % it_dir
if os.path.isfile(acc_file):
print('%s already generated.' % acc_file)
else:
# basenji test
basenji_cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
basenji_cmd += ' conda activate %s;' % options.conda_env
basenji_cmd += ' basenji_test.py'
basenji_cmd += ' -o %s/test_train' % it_dir
if options.rc:
basenji_cmd += ' --rc'
if options.shifts:
basenji_cmd += ' --shifts %s' % options.shifts
basenji_cmd += ' --split train'
basenji_cmd += ' %s' % params_file
basenji_cmd += ' %s/train/model_check.h5' % it_dir
basenji_cmd += ' %s/data' % it_dir
name = '%s-testtr-f%dc%d' % (options.name, fi, ci)
basenji_job = slurm.Job(
basenji_cmd,
name=name,
out_file='%s/test_train.out' % it_dir,
err_file='%s/test_train.err' % it_dir,
queue=options.queue,
cpu=1,
gpu=1,
mem=23000,
time='4:00:00')
jobs.append(basenji_job)
################################################################
# test best
################################################################
for ci in range(options.crosses):
for fi in range(num_folds):
it_dir = '%s/f%d_c%d' % (exp_dir, fi, ci)
# check if done
acc_file = '%s/test/acc.txt' % it_dir
if os.path.isfile(acc_file):
print('%s already generated.' % acc_file)
else:
# basenji test
basenji_cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
basenji_cmd += ' conda activate %s;' % options.conda_env
basenji_cmd += ' basenji_test.py'
basenji_cmd += ' -o %s/test' % it_dir
if options.rc:
basenji_cmd += ' --rc'
if options.shifts:
basenji_cmd += ' --shifts %s' % options.shifts
basenji_cmd += ' %s' % params_file
basenji_cmd += ' %s/train/model_best.h5' % it_dir
basenji_cmd += ' %s/data' % it_dir
name = '%s-test-f%dc%d' % (options.name, fi, ci)
basenji_job = slurm.Job(basenji_cmd,
name=name,
out_file='%s/test.out' % it_dir,
err_file='%s/test.err' % it_dir,
queue=options.queue,
cpu=1,
gpu=1,
mem=23000,
time='4:00:00')
jobs.append(basenji_job)
################################################################
# test best specificity
################################################################
if options.specificity:
for ci in range(options.crosses):
for fi in range(num_folds):
it_dir = '%s/f%d_c%d' % (exp_dir, fi, ci)
# check if done
acc_file = '%s/test_spec/acc.txt' % it_dir
if os.path.isfile(acc_file):
print('%s already generated.' % acc_file)
else:
# basenji test
basenji_cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
basenji_cmd += ' conda activate %s;' % options.conda_env
basenji_cmd += ' basenji_test_specificity.py'
basenji_cmd += ' -o %s/test_spec' % it_dir
if options.rc:
basenji_cmd += ' --rc'
if options.shifts:
basenji_cmd += ' --shifts %s' % options.shifts
basenji_cmd += ' %s' % params_file
basenji_cmd += ' %s/train/model_best.h5' % it_dir
basenji_cmd += ' %s/data' % it_dir
name = '%s-spec-f%dc%d' % (options.name, fi, ci)
basenji_job = slurm.Job(
basenji_cmd,
name=name,
out_file='%s/test_spec.out' % it_dir,
err_file='%s/test_spec.err' % it_dir,
queue=options.queue,
cpu=1,
gpu=1,
mem=60000,
time='6:00:00')
jobs.append(basenji_job)
slurm.multi_run(jobs, verbose=True)
if options.ref_dir is not None:
# classification or regression
with open('%s/f0_c0/test/acc.txt' % exp_dir) as test0_open:
header = test0_open.readline().split()
if 'pearsonr' in header:
metric = 'pearsonr'
else:
metric = 'auprc'
################################################################
# compare checkpoint on training set
################################################################
if options.train:
ref_glob_str = '%s/*/test_train/acc.txt' % options.ref_dir
ref_cors, ref_mean, ref_stdm = read_metrics(ref_glob_str, metric)
exp_glob_str = '%s/*/test_train/acc.txt' % exp_dir
exp_cors, exp_mean, exp_stdm = read_metrics(exp_glob_str, metric)
mwp, tp = stat_tests(ref_cors, exp_cors, options.alternative)
print('\nTrain:')
print('%12s %s: %.4f (%.4f)' %
(options.label1, metric, ref_mean, ref_stdm))
print('%12s %s: %.4f (%.4f)' %
(options.label2, metric, exp_mean, exp_stdm))
print('Mann-Whitney U p-value: %.3g' % mwp)
print('T-test p-value: %.3g' % tp)
if options.out_stem is not None:
jointplot(ref_cors, exp_cors,
'%s_train.pdf' % options.out_stem, options.label1,
options.label2)
################################################################
# compare best on test set
################################################################
ref_glob_str = '%s/*/test/acc.txt' % options.ref_dir
ref_cors, ref_mean, ref_stdm = read_metrics(ref_glob_str, metric)
exp_glob_str = '%s/*/test/acc.txt' % exp_dir
exp_cors, exp_mean, exp_stdm = read_metrics(exp_glob_str, metric)
mwp, tp = stat_tests(ref_cors, exp_cors, options.alternative)
print('\nTest:')
print('%12s %s: %.4f (%.4f)' %
(options.label1, metric, ref_mean, ref_stdm))
print('%12s %s: %.4f (%.4f)' %
(options.label2, metric, exp_mean, exp_stdm))
print('Mann-Whitney U p-value: %.3g' % mwp)
print('T-test p-value: %.3g' % tp)
if options.out_stem is not None:
jointplot(ref_cors, exp_cors, '%s_test.pdf' % options.out_stem,
options.label1, options.label2)
################################################################
# compare best on test set specificity
################################################################
if options.specificity:
ref_glob_str = '%s/*/test_spec/acc.txt' % options.ref_dir
ref_cors, ref_mean, ref_stdm = read_metrics(ref_glob_str, metric)
exp_glob_str = '%s/*/test_spec/acc.txt' % exp_dir
exp_cors, exp_mean, exp_stdm = read_metrics(exp_glob_str, metric)
mwp, tp = stat_tests(ref_cors, exp_cors, options.alternative)
print('\nSpecificity:')
print('%12s %s: %.4f (%.4f)' %
(options.label1, metric, ref_mean, ref_stdm))
print('%12s %s: %.4f (%.4f)' %
(options.label2, metric, exp_mean, exp_stdm))
print('Mann-Whitney U p-value: %.3g' % mwp)
print('T-test p-value: %.3g' % tp)
if options.out_stem is not None:
jointplot(ref_cors, exp_cors, '%s_spec.pdf' % options.out_stem,
options.label1, options.label2)
def main():
usage = (
"usage: %prog [options] <params_file> <model_file> <genes_hdf5_file>"
" <vcf_file>")
parser = OptionParser(usage)
parser.add_option(
"-a",
dest="all_sed",
default=False,
action="store_true",
help=
"Print all variant-gene pairs, as opposed to only nonzero [Default: %default]",
)
parser.add_option(
"-b",
dest="batch_size",
default=None,
type="int",
help="Batch size [Default: %default]",
)
parser.add_option(
"-c",
dest="csv",
default=False,
action="store_true",
help="Print table as CSV [Default: %default]",
)
parser.add_option(
"-g",
dest="genome_file",
default="%s/data/human.hg19.genome" % os.environ["BASENJIDIR"],
help="Chromosome lengths file [Default: %default]",
)
parser.add_option(
"-o",
dest="out_dir",
default="sed",
help="Output directory for tables and plots [Default: %default]",
)
parser.add_option(
"-p",
dest="processes",
default=2,
type="int",
help="Number of parallel processes to run [Default: %default]",
)
parser.add_option(
"--pseudo",
dest="log_pseudo",
default=0.125,
type="float",
help="Log2 pseudocount [Default: %default]",
)
parser.add_option(
"-q",
dest="queue",
default="k80",
help="SLURM queue on which to run the jobs [Default: %default]",
)
parser.add_option(
"-r",
dest="tss_radius",
default=0,
type="int",
help=
"Radius of bins considered to quantify TSS transcription [Default: %default]",
)
parser.add_option(
"--rc",
dest="rc",
default=False,
action="store_true",
help=
"Average the forward and reverse complement predictions when testing [Default: %default]",
)
parser.add_option(
"--shifts",
dest="shifts",
default="0",
help="Ensemble prediction shifts [Default: %default]",
)
parser.add_option(
"-t",
dest="targets_file",
default=None,
help="File specifying target indexes and labels in table format.",
)
parser.add_option(
"--ti",
dest="track_indexes",
help="Comma-separated list of target indexes to output BigWig tracks",
)
parser.add_option(
"-u",
dest="penultimate",
default=False,
action="store_true",
help="Compute SED in the penultimate layer [Default: %default]",
)
parser.add_option(
"-x",
dest="tss_table",
default=False,
action="store_true",
help="Print TSS table in addition to gene [Default: %default]",
)
(options, args) = parser.parse_args()
if len(args) != 4:
parser.error(
"Must provide parameters and model files, genes HDF5 file, and QTL VCF"
" file")
else:
params_file = args[0]
model_file = args[1]
genes_hdf5_file = args[2]
vcf_file = args[3]
#######################################################
# prep work
# output directory
if os.path.isdir(options.out_dir):
shutil.rmtree(options.out_dir)
os.mkdir(options.out_dir)
# pickle options
options_pkl_file = "%s/options.pkl" % options.out_dir
options_pkl = open(options_pkl_file, "wb")
pickle.dump(options, options_pkl)
options_pkl.close()
#######################################################
# launch worker threads
jobs = []
for pi in range(options.processes):
cmd = "source activate py3_gpu; basenji_sed.py %s %s %d" % (
options_pkl_file,
" ".join(args),
pi,
)
name = "sed_p%d" % pi
outf = "%s/job%d.out" % (options.out_dir, pi)
errf = "%s/job%d.err" % (options.out_dir, pi)
j = slurm.Job(cmd,
name,
outf,
errf,
queue=options.queue,
mem=30000,
time="4:0:0",
gpu=1)
jobs.append(j)
slurm.multi_run(jobs,
max_proc=options.processes,
verbose=True,
sleep_time=60)
#######################################################
# collect output
collect_table_multi("sed_gene.txt", options.out_dir, options.processes,
options.log_pseudo)
if options.tss_table:
collect_table("sed_tss.txt", options.out_dir, options.processes)
if options.track_indexes is not None:
if not os.path.isdir("%s/tracks" % options.out_dir):
os.mkdir("%s/tracks" % options.out_dir)
for track_file in glob.glob("%s/job*/tracks/*"):
track_base = os.path.split(track_file)[1]
os.rename(track_file,
"%s/tracks/%s" % (options.out_dir, track_base))
for pi in range(options.processes):
shutil.rmtree("%s/job%d" % (options.out_dir, pi))
def main():
usage = 'usage: %prog [options] <fasta_file> <targets_file>'
parser = OptionParser(usage)
parser.add_option('-b',
dest='blacklist_bed',
help='Set blacklist nucleotides to a baseline value.')
parser.add_option(
'--break',
dest='break_t',
default=786432,
type='int',
help='Break in half contigs above length [Default: %default]')
# parser.add_option('-c', dest='clip',
# default=None, type='float',
# help='Clip target values to have minimum [Default: %default]')
parser.add_option('-d',
dest='sample_pct',
default=1.0,
type='float',
help='Down-sample the segments')
parser.add_option('-g',
dest='gaps_file',
help='Genome assembly gaps BED [Default: %default]')
parser.add_option('-l',
dest='seq_length',
default=131072,
type='int',
help='Sequence length [Default: %default]')
parser.add_option(
'--limit',
dest='limit_bed',
help='Limit to segments that overlap regions in a BED file')
parser.add_option(
'--local',
dest='run_local',
default=False,
action='store_true',
help='Run jobs locally as opposed to on SLURM [Default: %default]')
parser.add_option('-o',
dest='out_dir',
default='data_out',
help='Output directory [Default: %default]')
parser.add_option('-p',
dest='processes',
default=None,
type='int',
help='Number parallel processes [Default: %default]')
parser.add_option('-r',
dest='seqs_per_tfr',
default=256,
type='int',
help='Sequences per TFRecord file [Default: %default]')
parser.add_option('--seed',
dest='seed',
default=44,
type='int',
help='Random seed [Default: %default]')
parser.add_option(
'--stride_train',
dest='stride_train',
default=1.,
type='float',
help='Stride to advance train sequences [Default: seq_length]')
parser.add_option(
'--stride_test',
dest='stride_test',
default=1.,
type='float',
help='Stride to advance valid and test sequences [Default: seq_length]'
)
parser.add_option(
'--soft',
dest='soft_clip',
default=False,
action='store_true',
help=
'Soft clip values, applying sqrt to the execess above the threshold [Default: %default]'
)
parser.add_option(
'-t',
dest='test_pct_or_chr',
default=0.05,
type='str',
help='Proportion of the data for testing [Default: %default]')
parser.add_option('-u',
dest='umap_bed',
help='Unmappable regions in BED format')
parser.add_option(
'--umap_t',
dest='umap_t',
default=0.3,
type='float',
help=
'Remove sequences with more than this unmappable bin % [Default: %default]'
)
parser.add_option(
'--umap_set',
dest='umap_set',
default=None,
type='float',
help=
'Set unmappable regions to this percentile in the sequences\' distribution of values'
)
parser.add_option('-w',
dest='pool_width',
default=128,
type='int',
help='Sum pool width [Default: %default]')
parser.add_option(
'-v',
dest='valid_pct_or_chr',
default=0.05,
type='str',
help='Proportion of the data for validation [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 2:
parser.error(
'Must provide FASTA and sample coverage labels and paths.')
else:
fasta_file = args[0]
targets_file = args[1]
random.seed(options.seed)
np.random.seed(options.seed)
if not os.path.isdir(options.out_dir):
os.mkdir(options.out_dir)
if options.stride_train <= 0 or options.stride_train > 1:
parser.error('Train stride =%f must be in [0,1]' %
options.stride_train)
if options.stride_test <= 0 or options.stride_test > 1:
parser.error('Test stride =%f must be in [0,1]' % options.stride_test)
################################################################
# define genomic contigs
################################################################
chrom_contigs = genome.load_chromosomes(fasta_file)
# remove gaps
if options.gaps_file:
chrom_contigs = genome.split_contigs(chrom_contigs, options.gaps_file)
# ditch the chromosomes for contigs
contigs = []
for chrom in chrom_contigs:
contigs += [
Contig(chrom, ctg_start, ctg_end)
for ctg_start, ctg_end in chrom_contigs[chrom]
]
# limit to a BED file
if options.limit_bed is not None:
contigs = limit_contigs(contigs, options.limit_bed)
# filter for large enough
contigs = [
ctg for ctg in contigs if ctg.end - ctg.start >= options.seq_length
]
# break up large contigs
if options.break_t is not None:
contigs = break_large_contigs(contigs, options.break_t)
# print contigs to BED file
ctg_bed_file = '%s/contigs.bed' % options.out_dir
write_seqs_bed(ctg_bed_file, contigs)
################################################################
# divide between train/valid/test
################################################################
try:
# convert to float pct
valid_pct = float(options.valid_pct_or_chr)
test_pct = float(options.test_pct_or_chr)
assert (0 <= valid_pct <= 1)
assert (0 <= test_pct <= 1)
# divide by pct
contig_sets = divide_contigs_pct(contigs, test_pct, valid_pct)
except (ValueError, AssertionError):
# divide by chr
valid_chr = options.valid_pct_or_chr
test_chr = options.test_pct_or_chr
contig_sets = divide_contigs_chr(contigs, test_chr, valid_chr)
train_contigs, valid_contigs, test_contigs = contig_sets
# rejoin broken contigs within set
train_contigs = rejoin_large_contigs(train_contigs)
valid_contigs = rejoin_large_contigs(valid_contigs)
test_contigs = rejoin_large_contigs(test_contigs)
################################################################
# define model sequences
################################################################
# stride sequences across contig
train_mseqs = contig_sequences(train_contigs,
options.seq_length,
options.stride_train,
label='train')
valid_mseqs = contig_sequences(valid_contigs,
options.seq_length,
options.stride_test,
label='valid')
test_mseqs = contig_sequences(test_contigs,
options.seq_length,
options.stride_test,
label='test')
# shuffle
random.shuffle(train_mseqs)
random.shuffle(valid_mseqs)
random.shuffle(test_mseqs)
# merge
mseqs = train_mseqs + valid_mseqs + test_mseqs
################################################################
# mappability
################################################################
if options.umap_bed is not None:
# annotate unmappable positions
mseqs_unmap = annotate_unmap(mseqs, options.umap_bed,
options.seq_length, options.pool_width)
# filter unmappable
mseqs_map_mask = (mseqs_unmap.mean(axis=1, dtype='float64') <
options.umap_t)
mseqs = [mseqs[i] for i in range(len(mseqs)) if mseqs_map_mask[i]]
mseqs_unmap = mseqs_unmap[mseqs_map_mask, :]
# write to file
unmap_npy = '%s/mseqs_unmap.npy' % options.out_dir
np.save(unmap_npy, mseqs_unmap)
# down-sample
if options.sample_pct < 1.0:
mseqs = random.sample(mseqs, int(options.sample_pct * len(contigs)))
# write sequences to BED
seqs_bed_file = '%s/sequences.bed' % options.out_dir
write_seqs_bed(seqs_bed_file, mseqs, True)
################################################################
# read sequence coverage values
################################################################
# read target datasets
targets_df = pd.read_table(targets_file, index_col=0)
seqs_cov_dir = '%s/seqs_cov' % options.out_dir
if not os.path.isdir(seqs_cov_dir):
os.mkdir(seqs_cov_dir)
read_jobs = []
for ti in range(targets_df.shape[0]):
genome_cov_file = targets_df['file'].iloc[ti]
seqs_cov_stem = '%s/%d' % (seqs_cov_dir, ti)
seqs_cov_file = '%s.h5' % seqs_cov_stem
clip_ti = None
if 'clip' in targets_df.columns:
clip_ti = targets_df['clip'].iloc[ti]
scale_ti = 1
if 'scale' in targets_df.columns:
scale_ti = targets_df['scale'].iloc[ti]
if os.path.isfile(seqs_cov_file):
print('Skipping existing %s' % seqs_cov_file, file=sys.stderr)
else:
cmd = 'basenji_data_read.py'
cmd += ' -w %d' % options.pool_width
cmd += ' -u %s' % targets_df['sum_stat'].iloc[ti]
if clip_ti is not None:
cmd += ' -c %f' % clip_ti
if options.soft_clip:
cmd += ' --soft'
cmd += ' -s %f' % scale_ti
if options.blacklist_bed:
cmd += ' -b %s' % options.blacklist_bed
cmd += ' %s' % genome_cov_file
cmd += ' %s' % seqs_bed_file
cmd += ' %s' % seqs_cov_file
if options.run_local:
cmd += ' &> %s.err' % seqs_cov_stem
read_jobs.append(cmd)
else:
j = slurm.Job(cmd,
name='read_t%d' % ti,
out_file='%s.out' % seqs_cov_stem,
err_file='%s.err' % seqs_cov_stem,
queue='standard,tbdisk',
mem=15000,
time='12:0:0')
read_jobs.append(j)
if options.run_local:
util.exec_par(read_jobs, options.processes, verbose=True)
else:
slurm.multi_run(read_jobs,
options.processes,
verbose=True,
launch_sleep=1,
update_sleep=5)
################################################################
# write TF Records
################################################################
# copy targets file
shutil.copy(targets_file, '%s/targets.txt' % options.out_dir)
# initialize TF Records dir
tfr_dir = '%s/tfrecords' % options.out_dir
if not os.path.isdir(tfr_dir):
os.mkdir(tfr_dir)
write_jobs = []
for tvt_set in ['train', 'valid', 'test']:
tvt_set_indexes = [
i for i in range(len(mseqs)) if mseqs[i].label == tvt_set
]
tvt_set_start = tvt_set_indexes[0]
tvt_set_end = tvt_set_indexes[-1] + 1
tfr_i = 0
tfr_start = tvt_set_start
tfr_end = min(tfr_start + options.seqs_per_tfr, tvt_set_end)
while tfr_start <= tvt_set_end:
tfr_stem = '%s/%s-%d' % (tfr_dir, tvt_set, tfr_i)
cmd = 'basenji_data_write.py'
cmd += ' -s %d' % tfr_start
cmd += ' -e %d' % tfr_end
if options.umap_bed is not None:
cmd += ' -u %s' % unmap_npy
if options.umap_set is not None:
cmd += ' --umap_set %f' % options.umap_set
cmd += ' %s' % fasta_file
cmd += ' %s' % seqs_bed_file
cmd += ' %s' % seqs_cov_dir
cmd += ' %s.tfr' % tfr_stem
if options.run_local:
cmd += ' &> %s.err' % tfr_stem
write_jobs.append(cmd)
else:
j = slurm.Job(cmd,
name='write_%s-%d' % (tvt_set, tfr_i),
out_file='%s.out' % tfr_stem,
err_file='%s.err' % tfr_stem,
queue='standard,tbdisk',
mem=15000,
time='12:0:0')
write_jobs.append(j)
# update
tfr_i += 1
tfr_start += options.seqs_per_tfr
tfr_end = min(tfr_start + options.seqs_per_tfr, tvt_set_end)
if options.run_local:
util.exec_par(write_jobs, options.processes, verbose=True)
else:
slurm.multi_run(write_jobs,
options.processes,
verbose=True,
launch_sleep=1,
update_sleep=5)
def main():
usage = 'usage: %prog [options] <params_file> <model_file>'
parser = OptionParser(usage)
# sad
parser.add_option('-f',
dest='genome_fasta',
default='%s/data/hg38.fa' % os.environ['BASENJIDIR'],
help='Genome FASTA for sequences [Default: %default]')
parser.add_option('--local',
dest='local',
default=1024,
type='int',
help='Local SAD score [Default: %default]')
parser.add_option('-n',
dest='norm_file',
default=None,
help='Normalize SAD scores')
parser.add_option(
'-o',
dest='out_dir',
default='sad_gtex',
help='Output directory for tables and plots [Default: %default]')
parser.add_option('--pseudo',
dest='log_pseudo',
default=1,
type='float',
help='Log2 pseudocount [Default: %default]')
parser.add_option(
'--rc',
dest='rc',
default=False,
action='store_true',
help=
'Average forward and reverse complement predictions [Default: %default]'
)
parser.add_option('--shifts',
dest='shifts',
default='0',
type='str',
help='Ensemble prediction shifts [Default: %default]')
parser.add_option(
'--stats',
dest='sad_stats',
default='SAD',
help='Comma-separated list of stats to save. [Default: %default]')
parser.add_option(
'-t',
dest='targets_file',
default=None,
type='str',
help='File specifying target indexes and labels in table format')
parser.add_option(
'--ti',
dest='track_indexes',
default=None,
type='str',
help='Comma-separated list of target indexes to output BigWig tracks')
parser.add_option(
'--threads',
dest='threads',
default=False,
action='store_true',
help='Run CPU math and output in a separate thread [Default: %default]'
)
parser.add_option(
'-u',
dest='penultimate',
default=False,
action='store_true',
help='Compute SED in the penultimate layer [Default: %default]')
# multi
parser.add_option('-e',
dest='conda_env',
default='tf2.2-gpu',
help='Anaconda environment [Default: %default]')
parser.add_option('-g',
dest='gtex_vcf_dir',
default='/home/drk/seqnn/data/gtex_fine/susie_pip90')
parser.add_option('--name',
dest='name',
default='gtex',
help='SLURM name prefix [Default: %default]')
parser.add_option('--max_proc',
dest='max_proc',
default=None,
type='int',
help='Maximum concurrent processes [Default: %default]')
parser.add_option('-p',
dest='processes',
default=None,
type='int',
help='Number of processes, passed by multi script. \
(Unused, but needs to appear as dummy.)')
parser.add_option(
'-q',
dest='queue',
default='gtx1080ti',
help='SLURM queue on which to run the jobs [Default: %default]')
parser.add_option(
'-r',
dest='restart',
default=False,
action='store_true',
help='Restart a partially completed job [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 2:
parser.error('Must provide parameters and model files')
else:
params_file = args[0]
model_file = args[1]
#######################################################
# prep work
# output directory
if not options.restart:
if os.path.isdir(options.out_dir):
print('Please remove %s' % options.out_dir, file=sys.stderr)
exit(1)
os.mkdir(options.out_dir)
# pickle options
options_pkl_file = '%s/options.pkl' % options.out_dir
options_pkl = open(options_pkl_file, 'wb')
pickle.dump(options, options_pkl)
options_pkl.close()
#######################################################
# predict
cmd_base = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
cmd_base += ' conda activate %s;' % options.conda_env
cmd_base += ' basenji_sad.py %s %s %s' % (options_pkl_file, params_file,
model_file)
jobs = []
for gtex_pos_vcf in glob.glob('%s/*_pos.vcf' % options.gtex_vcf_dir):
# positive job
job_base = os.path.splitext(os.path.split(gtex_pos_vcf)[1])[0]
out_dir = '%s/%s' % (options.out_dir, job_base)
if not options.restart or not os.path.isfile('%s/sad.h5' % out_dir):
cmd = '%s -o %s %s' % (cmd_base, out_dir, gtex_pos_vcf)
name = '%s_%s' % (options.name, job_base)
j = slurm.Job(cmd,
name,
'%s.out' % out_dir,
'%s.err' % out_dir,
queue=options.queue,
gpu=1,
mem=22000,
time='1-0:0:0')
jobs.append(j)
# negative job
gtex_neg_vcf = gtex_pos_vcf.replace('_pos.', '_neg.')
job_base = os.path.splitext(os.path.split(gtex_neg_vcf)[1])[0]
out_dir = '%s/%s' % (options.out_dir, job_base)
if not options.restart or not os.path.isfile('%s/sad.h5' % out_dir):
cmd = '%s -o %s %s' % (cmd_base, out_dir, gtex_neg_vcf)
name = '%s_%s' % (options.name, job_base)
j = slurm.Job(cmd,
name,
'%s.out' % out_dir,
'%s.err' % out_dir,
queue=options.queue,
gpu=1,
mem=22000,
time='1-0:0:0')
jobs.append(j)
slurm.multi_run(jobs,
max_proc=options.max_proc,
verbose=True,
launch_sleep=10,
update_sleep=60)
#######################################################
# classify
cmd_base = 'basenji_bench_classify.py -i 100 -p 2 -r 44 -s'
jobs = []
for gtex_pos_vcf in glob.glob('%s/*_pos.vcf' % options.gtex_vcf_dir):
tissue = os.path.splitext(os.path.split(gtex_pos_vcf)[1])[0][:-4]
sad_pos = '%s/%s_pos/sad.h5' % (options.out_dir, tissue)
sad_neg = '%s/%s_neg/sad.h5' % (options.out_dir, tissue)
out_dir = '%s/%s_class' % (options.out_dir, tissue)
if not options.restart or not os.path.isfile('%s/stats.txt' % out_dir):
cmd = '%s -o %s %s %s' % (cmd_base, out_dir, sad_pos, sad_neg)
j = slurm.Job(cmd,
tissue,
'%s.out' % out_dir,
'%s.err' % out_dir,
queue='standard',
cpu=2,
mem=22000,
time='1-0:0:0')
jobs.append(j)
slurm.multi_run(jobs, verbose=True)
def main():
usage = 'usage: %prog [options] <exp_dir> <params_file> <data1_dir> ...'
parser = OptionParser(usage)
parser.add_option('-a',
'--alt',
dest='alternative',
default='two-sided',
help='Statistical test alternative [Default: %default]')
parser.add_option('-c',
dest='crosses',
default=1,
type='int',
help='Number of cross-fold rounds [Default:%default]')
parser.add_option('-d',
dest='dataset_i',
default=None,
type='int',
help='Dataset index [Default:%default]')
parser.add_option('--d_ref',
dest='dataset_ref_i',
default=None,
type='int',
help='Reference Dataset index [Default:%default]')
parser.add_option('-e',
dest='conda_env',
default='tf2-gpu',
help='Anaconda environment [Default: %default]')
parser.add_option('-f',
dest='fold_subset',
default=None,
type='int',
help='Run a subset of folds [Default:%default]')
parser.add_option('--label_exp',
dest='label_exp',
default='Experiment',
help='Experiment label [Default: %default]')
parser.add_option('--label_ref',
dest='label_ref',
default='Reference',
help='Reference label [Default: %default]')
parser.add_option('-m',
dest='metric',
default=None,
help='Train/test metric [Default: Pearsonr or AUPRC]')
parser.add_option('--name',
dest='name',
default='test',
help='SLURM name prefix [Default: %default]')
parser.add_option('-o',
dest='out_stem',
default=None,
help='Output plot stem [Default: %default]')
parser.add_option('-q', dest='queue', default='gtx1080ti')
parser.add_option('-r',
dest='ref_dir',
default=None,
help='Reference directory for statistical tests')
parser.add_option(
'--rc',
dest='rc',
default=False,
action='store_true',
help=
'Average forward and reverse complement predictions [Default: %default]'
)
parser.add_option('--shifts',
dest='shifts',
default='0',
type='str',
help='Ensemble prediction shifts [Default: %default]')
parser.add_option('--spec',
dest='specificity',
default=False,
action='store_true',
help='Test specificity [Default: %default]')
parser.add_option('--train',
dest='train',
default=False,
action='store_true',
help='Test on the training set, too [Default: %default]')
(options, args) = parser.parse_args()
if len(args) < 3:
parser.error('Must provide parameters file and data directory')
else:
exp_dir = args[0]
params_file = args[1]
data_dirs = [os.path.abspath(arg) for arg in args[2:]]
# read data parameters
data_stats_file = '%s/statistics.json' % data_dirs[0]
with open(data_stats_file) as data_stats_open:
data_stats = json.load(data_stats_open)
if options.dataset_i is None:
head_i = 0
else:
head_i = options.dataset_i
# count folds
num_folds = len([dkey for dkey in data_stats if dkey.startswith('fold')])
# subset folds
if options.fold_subset is not None:
num_folds = min(options.fold_subset, num_folds)
################################################################
# test check
################################################################
jobs = []
if options.train:
for ci in range(options.crosses):
for fi in range(num_folds):
it_dir = '%s/f%d_c%d' % (exp_dir, fi, ci)
if options.dataset_i is None:
out_dir = '%s/test_train' % it_dir
model_file = '%s/train/model_check.h5' % it_dir
else:
out_dir = '%s/test%d_train' % (it_dir, options.dataset_i)
model_file = '%s/train/model%d_check.h5' % (
it_dir, options.dataset_i)
# check if done
acc_file = '%s/acc.txt' % out_dir
if os.path.isfile(acc_file):
# print('%s already generated.' % acc_file)
pass
else:
cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
cmd += ' conda activate %s;' % options.conda_env
cmd += ' basenji_test.py'
cmd += ' --head %d' % head_i
cmd += ' -o %s' % out_dir
if options.rc:
cmd += ' --rc'
if options.shifts:
cmd += ' --shifts %s' % options.shifts
cmd += ' --split train'
cmd += ' %s' % params_file
cmd += ' %s' % model_file
cmd += ' %s/data%d' % (it_dir, head_i)
name = '%s-testtr-f%dc%d' % (options.name, fi, ci)
j = slurm.Job(cmd,
name=name,
out_file='%s.out' % out_dir,
err_file='%s.err' % out_dir,
queue=options.queue,
cpu=1,
gpu=1,
mem=23000,
time='4:00:00')
jobs.append(j)
################################################################
# test best
################################################################
for ci in range(options.crosses):
for fi in range(num_folds):
it_dir = '%s/f%d_c%d' % (exp_dir, fi, ci)
if options.dataset_i is None:
out_dir = '%s/test' % it_dir
model_file = '%s/train/model_best.h5' % it_dir
else:
out_dir = '%s/test%d' % (it_dir, options.dataset_i)
model_file = '%s/train/model%d_best.h5' % (it_dir,
options.dataset_i)
# check if done
acc_file = '%s/acc.txt' % out_dir
if os.path.isfile(acc_file):
# print('%s already generated.' % acc_file)
pass
else:
# basenji test
cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
cmd += ' conda activate %s;' % options.conda_env
cmd += ' basenji_test.py'
cmd += ' --head %d' % head_i
cmd += ' -o %s' % out_dir
if options.rc:
cmd += ' --rc'
if options.shifts:
cmd += ' --shifts %s' % options.shifts
cmd += ' %s' % params_file
cmd += ' %s' % model_file
cmd += ' %s/data%d' % (it_dir, head_i)
name = '%s-test-f%dc%d' % (options.name, fi, ci)
j = slurm.Job(cmd,
name=name,
out_file='%s.out' % out_dir,
err_file='%s.err' % out_dir,
queue=options.queue,
cpu=1,
gpu=1,
mem=23000,
time='4:00:00')
jobs.append(j)
################################################################
# test best specificity
################################################################
if options.specificity:
for ci in range(options.crosses):
for fi in range(num_folds):
it_dir = '%s/f%d_c%d' % (exp_dir, fi, ci)
if options.dataset_i is None:
out_dir = '%s/test_spec' % it_dir
model_file = '%s/train/model_best.h5' % it_dir
else:
out_dir = '%s/test%d_spec' % (it_dir, options.dataset_i)
model_file = '%s/train/model%d_best.h5' % (
it_dir, options.dataset_i)
# check if done
acc_file = '%s/acc.txt' % out_dir
if os.path.isfile(acc_file):
# print('%s already generated.' % acc_file)
pass
else:
# basenji test
cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
cmd += ' conda activate %s;' % options.conda_env
cmd += ' basenji_test_specificity.py'
cmd += ' --head %d' % head_i
cmd += ' -o %s' % out_dir
if options.rc:
cmd += ' --rc'
if options.shifts:
cmd += ' --shifts %s' % options.shifts
cmd += ' %s' % params_file
cmd += ' %s' % model_file
cmd += ' %s/data%d' % (it_dir, head_i)
name = '%s-spec-f%dc%d' % (options.name, fi, ci)
j = slurm.Job(cmd,
name=name,
out_file='%s.out' % out_dir,
err_file='%s.err' % out_dir,
queue=options.queue,
cpu=1,
gpu=1,
mem=75000,
time='6:00:00')
jobs.append(j)
slurm.multi_run(jobs, verbose=True)
if options.dataset_i is None:
test_prefix = 'test'
else:
test_prefix = 'test%d' % options.dataset_i
if options.dataset_ref_i is None:
test_ref_prefix = 'test'
else:
test_ref_prefix = 'test%d' % options.dataset_ref_i
# classification or regression
if options.metric is None:
with open('%s/f0_c0/%s/acc.txt' %
(exp_dir, test_prefix)) as test0_open:
header = test0_open.readline().split()
if 'pearsonr' in header:
options.metric = 'pearsonr'
else:
options.metric = 'auprc'
################################################################
# compare checkpoint on training set
################################################################
if options.train:
exp_glob_str = '%s/*/%s_train/acc.txt' % (exp_dir, test_prefix)
exp_cors, exp_mean, exp_stdm = read_metrics(exp_glob_str,
options.metric)
if options.ref_dir is not None:
ref_glob_str = '%s/*/%s_train/acc.txt' % (options.ref_dir,
test_ref_prefix)
ref_cors, ref_mean, ref_stdm = read_metrics(
ref_glob_str, options.metric)
mwp, tp = stat_tests(ref_cors, exp_cors, options.alternative)
print('\nTrain:')
print('%12s %s: %.4f (%.4f)' %
(options.label_exp, options.metric, exp_mean, exp_stdm))
if options.ref_dir is not None:
print('%12s %s: %.4f (%.4f)' %
(options.label_ref, options.metric, ref_mean, ref_stdm))
print('Mann-Whitney U p-value: %.3g' % mwp)
print('T-test p-value: %.3g' % tp)
if options.out_stem is not None:
jointplot(ref_cors, exp_cors,
'%s_train.pdf' % options.out_stem, options.label_ref,
options.label_exp)
################################################################
# compare best on test set
################################################################
exp_glob_str = '%s/*/%s/acc.txt' % (exp_dir, test_prefix)
exp_cors, exp_mean, exp_stdm = read_metrics(exp_glob_str, options.metric)
if options.ref_dir is not None:
ref_glob_str = '%s/*/%s/acc.txt' % (options.ref_dir, test_ref_prefix)
ref_cors, ref_mean, ref_stdm = read_metrics(ref_glob_str,
options.metric)
mwp, tp = stat_tests(ref_cors, exp_cors, options.alternative)
print('\nTest:')
print('%12s %s: %.4f (%.4f)' %
(options.label_exp, options.metric, exp_mean, exp_stdm))
if options.ref_dir is not None:
print('%12s %s: %.4f (%.4f)' %
(options.label_ref, options.metric, ref_mean, ref_stdm))
print('Mann-Whitney U p-value: %.3g' % mwp)
print('T-test p-value: %.3g' % tp)
if options.out_stem is not None:
jointplot(ref_cors, exp_cors, '%s_test.pdf' % options.out_stem,
options.label_ref, options.label_exp)
################################################################
# compare best on test set specificity
################################################################
if options.specificity:
exp_glob_str = '%s/*/%s_spec/acc.txt' % (exp_dir, test_prefix)
exp_cors, exp_mean, exp_stdm = read_metrics(exp_glob_str,
options.metric)
if options.ref_dir is not None:
ref_glob_str = '%s/*/%s_spec/acc.txt' % (options.ref_dir,
test_ref_prefix)
ref_cors, ref_mean, ref_stdm = read_metrics(
ref_glob_str, options.metric)
mwp, tp = stat_tests(ref_cors, exp_cors, options.alternative)
print('\nSpecificity:')
print('%12s %s: %.4f (%.4f)' %
(options.label_exp, options.metric, exp_mean, exp_stdm))
if options.ref_dir is not None:
print('%12s %s: %.4f (%.4f)' %
(options.label_ref, options.metric, ref_mean, ref_stdm))
print('Mann-Whitney U p-value: %.3g' % mwp)
print('T-test p-value: %.3g' % tp)
if options.out_stem is not None:
jointplot(ref_cors, exp_cors, '%s_spec.pdf' % options.out_stem,
options.label_ref, options.label_exp)
def main():
usage = 'usage: %prog [options] <params_file> <seed_model> <data_file>'
parser = OptionParser(usage)
parser.add_option(
'-e',
dest='num_epochs',
default=4,
type='int',
help='Number of epochs to train models [Default: %default]')
parser.add_option('-n',
dest='num_models',
default=3,
type='int',
help='Number of models to train [Default: %default]')
parser.add_option(
'-o',
dest='out_dir',
default='seqnn_avg',
help='Output directory in which to train [Default: %default]')
parser.add_option(
'-s',
dest='num_steps',
default=None,
type='int',
help='Number of steps to train models [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 3:
parser.error('Must provide parameters, seed model, and data')
else:
params_file = args[0]
seed_model = args[1]
data_file = args[2]
if not os.path.isdir(options.out_dir):
os.mkdir(options.out_dir)
jobs = []
for mi in range(options.num_models):
model_dir = '%s/m%d' % (options.out_dir, mi)
cmd = 'source activate py3_gpu;'
cmd += ' basenji_train.py'
cmd += ' --rc --shifts "3,2,1,0,-1,-2,-3"'
cmd += ' --logdir %s' % model_dir
cmd += ' --check_all'
cmd += ' --num_train_epochs %d' % options.num_epochs
cmd += ' --restart %s' % seed_model
cmd += ' --params %s' % params_file
cmd += ' --data %s' % data_file
j = slurm.Job(cmd,
name=model_dir,
out_file='%s.out' % model_dir,
err_file='%s.err' % model_dir,
queue='gtx1080ti',
gpu=1,
cpu=1,
time='4-0:0:0',
mem=30000)
jobs.append(j)
slurm.multi_run(jobs, verbose=True)
def main():
usage = 'usage: %prog [options] <fasta_file> <targets_file>'
parser = OptionParser(usage)
parser.add_option('-b', dest='limit_bed',
help='Limit to segments that overlap regions in a BED file')
# parser.add_option('-c', dest='clip',
# default=None, type='float',
# help='Clip target values to have minimum [Default: %default]')
parser.add_option('-d', dest='sample_pct',
default=1.0, type='float',
help='Down-sample the segments')
parser.add_option('-g', dest='gaps_file',
help='Genome assembly gaps BED [Default: %default]')
parser.add_option('-l', dest='seq_length',
default=131072, type='int',
help='Sequence length [Default: %default]')
parser.add_option('--local', dest='run_local',
default=False, action='store_true',
help='Run jobs locally as opposed to on SLURM [Default: %default]')
parser.add_option('-o', dest='out_dir',
default='data_out',
help='Output directory [Default: %default]')
parser.add_option('-p', dest='processes',
default=None, type='int',
help='Number parallel processes [Default: %default]')
parser.add_option('--seed', dest='seed',
default=44, type='int',
help='Random seed [Default: %default]')
parser.add_option('--stride_train', dest='stride_train',
default=1., type='float',
help='Stride to advance train sequences [Default: seq_length]')
parser.add_option('--stride_test', dest='stride_test',
default=1., type='float',
help='Stride to advance valid and test sequences [Default: seq_length]')
parser.add_option('-r', dest='seqs_per_tfr',
default=256, type='int',
help='Sequences per TFRecord file [Default: %default]')
parser.add_option('-t', dest='test_pct',
default=0.05, type='float',
help='Proportion of the data for testing [Default: %default]')
parser.add_option('-u', dest='unmap_bed',
help='Unmappable segments to set to NA')
parser.add_option('--unmap_t', dest='unmap_t',
default=0.3, type='float',
help='Remove sequences with more than this unmappable bin % [Default: %default]')
parser.add_option('-w', dest='pool_width',
default=128, type='int',
help='Sum pool width [Default: %default]')
parser.add_option('-v', dest='valid_pct',
default=0.05, type='float',
help='Proportion of the data for validation [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 2:
parser.error('Must provide FASTA and sample coverage labels and paths.')
else:
fasta_file = args[0]
targets_file = args[1]
random.seed(options.seed)
np.random.seed(options.seed)
if not os.path.isdir(options.out_dir):
os.mkdir(options.out_dir)
################################################################
# define genomic contigs
################################################################
chrom_contigs = basenji.genome.load_chromosomes(fasta_file)
# remove gaps
if options.gaps_file:
chrom_contigs = basenji.genome.split_contigs(chrom_contigs,
options.gaps_file)
# ditch the chromosomes for contigs
contigs = []
for chrom in chrom_contigs:
contigs += [Contig(chrom, ctg_start, ctg_end)
for ctg_start, ctg_end in chrom_contigs[chrom]]
# limit to a BED file
if options.limit_bed is not None:
contigs = limit_contigs(contigs, options.limit_bed)
# filter for large enough
contigs = [ctg for ctg in contigs if ctg.end - ctg.start >= options.seq_length]
# down-sample
if options.sample_pct < 1.0:
contigs = random.sample(contigs, int(options.sample_pct*len(contigs)))
# print contigs to BED file
ctg_bed_file = '%s/contigs.bed' % options.out_dir
write_seqs_bed(ctg_bed_file, contigs)
################################################################
# divide between train/valid/test
################################################################
contig_sets = divide_contigs(contigs, options.test_pct, options.valid_pct)
train_contigs, valid_contigs, test_contigs = contig_sets
################################################################
# define model sequences
################################################################
# stride sequences across contig
train_mseqs = contig_sequences(train_contigs, options.seq_length, options.stride_train)
valid_mseqs = contig_sequences(valid_contigs, options.seq_length, options.stride_test)
test_mseqs = contig_sequences(test_contigs, options.seq_length, options.stride_test)
# shuffle
random.shuffle(train_mseqs)
random.shuffle(valid_mseqs)
random.shuffle(test_mseqs)
# merge
mseqs = train_mseqs + valid_mseqs + test_mseqs
mseqs_labels = ['train']*len(train_mseqs) + ['valid']*len(valid_mseqs) + ['test']*len(test_mseqs)
################################################################
# mappability
################################################################
if options.unmap_bed is not None:
# annotate unmappable positions
mseqs_unmap = annotate_unmap(mseqs, options.unmap_bed,
options.seq_length, options.pool_width)
# filter unmappable
mseqs_map_mask = (mseqs_unmap.mean(axis=1, dtype='float64') < options.unmap_t)
mseqs = [mseqs[i] for i in range(len(mseqs)) if mseqs_map_mask[i]]
mseqs_labels = [mseqs_labels[i] for i in range(len(mseqs_labels)) if mseqs_map_mask[i]]
mseqs_unmap = mseqs_unmap[mseqs_map_mask,:]
# write to file
unmap_npy = '%s/mseqs_unmap.npy' % options.out_dir
np.save(unmap_npy, mseqs_unmap)
# write sequences to BED
seqs_bed_file = '%s/sequences.bed' % options.out_dir
write_seqs_bed(seqs_bed_file, mseqs, mseqs_labels)
################################################################
# read sequence coverage values
################################################################
# read target datasets
targets_df = pd.read_table(targets_file)
seqs_cov_dir = '%s/seqs_cov' % options.out_dir
if not os.path.isdir(seqs_cov_dir):
os.mkdir(seqs_cov_dir)
read_jobs = []
for ti in range(targets_df.shape[0]):
genome_cov_file = targets_df['file'].iloc[ti]
seqs_cov_stem = '%s/%d' % (seqs_cov_dir, ti)
seqs_cov_file = '%s.h5' % seqs_cov_stem
if os.path.isfile(seqs_cov_file):
print('Skipping existing %s' % seqs_cov_file, file=sys.stderr)
else:
cmd = 'basenji_data_read.py'
cmd += ' -w %d' % options.pool_width
cmd += ' %s' % genome_cov_file
cmd += ' %s' % seqs_bed_file
cmd += ' %s' % seqs_cov_file
if options.run_local:
cmd += ' &> %s.err' % seqs_cov_stem
read_jobs.append(cmd)
else:
j = slurm.Job(cmd,
name='read_t%d' % ti,
out_file='%s.out' % seqs_cov_stem,
err_file='%s.err' % seqs_cov_stem,
queue='standard,tbdisk', mem=15000, time='12:0:0')
read_jobs.append(j)
if options.run_local:
util.exec_par(read_jobs, options.processes, verbose=True)
else:
slurm.multi_run(read_jobs, options.processes, verbose=True, sleep_time=1)
################################################################
# write TF Records
################################################################
tfr_dir = '%s/tfrecords' % options.out_dir
if not os.path.isdir(tfr_dir):
os.mkdir(tfr_dir)
write_jobs = []
for tvt_set in ['train', 'valid', 'test']:
tvt_set_indexes = [i for i in range(len(mseqs_labels)) if mseqs_labels[i] == tvt_set]
tvt_set_start = tvt_set_indexes[0]
tvt_set_end = tvt_set_indexes[-1]
tfr_i = 0
tfr_start = tvt_set_start
tfr_end = min(tfr_start+options.seqs_per_tfr, tvt_set_end)
while tfr_start <= tvt_set_end:
tfr_stem = '%s/%s-%d' % (tfr_dir, tvt_set, tfr_i)
cmd = 'basenji_data_write.py'
cmd += ' -s %d' % tfr_start
cmd += ' -e %d' % tfr_end
if options.unmap_bed is not None:
cmd += ' -u %s' % unmap_npy
cmd += ' %s' % fasta_file
cmd += ' %s' % seqs_bed_file
cmd += ' %s' % seqs_cov_dir
cmd += ' %s.tfr' % tfr_stem
if options.run_local:
cmd += ' &> %s.err' % tfr_stem
write_jobs.append(cmd)
else:
j = slurm.Job(cmd,
name='write_%s-%d' % (tvt_set, tfr_i),
out_file='%s.out' % tfr_stem,
err_file='%s.err' % tfr_stem,
queue='standard,tbdisk', mem=15000, time='12:0:0')
write_jobs.append(j)
# update
tfr_i += 1
tfr_start += options.seqs_per_tfr
tfr_end = min(tfr_start+options.seqs_per_tfr, tvt_set_end)
if options.run_local:
util.exec_par(write_jobs, options.processes, verbose=True)
else:
slurm.multi_run(write_jobs, options.processes, verbose=True, sleep_time=1)
def main():
usage = 'usage: %prog [options] <params_file> <data_dir>'
parser = OptionParser(usage)
# train
train_options = OptionGroup(parser, 'basenji_train.py options')
train_options.add_option(
'-k',
dest='keras_fit',
default=False,
action='store_true',
help='Train with Keras fit method [Default: %default]')
train_options.add_option(
'-o',
dest='out_dir',
default='train_out',
help='Output directory for test statistics [Default: %default]')
train_options.add_option(
'--restore',
dest='restore',
help='Restore model and continue training [Default: %default]')
train_options.add_option(
'--trunk',
dest='trunk',
default=False,
action='store_true',
help='Restore only model trunk [Default: %default]')
train_options.add_option(
'--tfr_train',
dest='tfr_train_pattern',
default='train-*.tfr',
help=
'Training TFRecord pattern string appended to data_dir [Default: %default]'
)
train_options.add_option(
'--tfr_eval',
dest='tfr_eval_pattern',
default='valid-*.tfr',
help=
'Evaluation TFRecord pattern string appended to data_dir [Default: %default]'
)
parser.add_option_group(train_options)
# test
test_options = OptionGroup(parser, 'basenji_test.py options')
test_options.add_option(
'--rc',
dest='rc',
default=False,
action='store_true',
help=
'Average forward and reverse complement predictions [Default: %default]'
)
test_options.add_option(
'--shifts',
dest='shifts',
default='0',
type='str',
help='Ensemble prediction shifts [Default: %default]')
parser.add_option_group(test_options)
# multi
rep_options = OptionGroup(parser, 'replication options')
rep_options.add_option('-e',
dest='conda_env',
default='tf2-gpu',
help='Anaconda environment [Default: %default]')
rep_options.add_option('--name',
dest='name',
default='reps',
help='SLURM name prefix [Default: %default]')
rep_options.add_option('-p',
dest='processes',
default=None,
type='int',
help='Number of processes, passed by multi script')
rep_options.add_option(
'-q',
dest='queue',
default='gtx1080ti',
help='SLURM queue on which to run the jobs [Default: %default]')
rep_options.add_option('-r',
dest='restart',
default=False,
action='store_true')
parser.add_option_group(rep_options)
(options, args) = parser.parse_args()
if len(args) != 2:
parser.error('Must provide parameters and data directory.')
else:
params_file = os.path.abspath(args[0])
data_dir = os.path.abspath(args[1])
# read model parameters
with open(params_file) as params_open:
params = json.load(params_open)
params_train = params['train']
#######################################################
# prep work
if not options.restart and os.path.isdir(options.out_dir):
print('Output directory %s exists. Please remove.' % options.out_dir)
exit(1)
if not os.path.isdir(options.out_dir):
os.mkdir(options.out_dir)
#######################################################
# train
jobs = []
for pi in range(options.processes):
rep_dir = '%s/%d' % (options.out_dir, pi)
if options.restart and os.path.isdir(rep_dir):
print('%s found and skipped.' % rep_dir)
else:
os.mkdir(rep_dir)
cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
cmd += ' conda activate %s;' % options.conda_env
cmd += ' echo $HOSTNAME;'
cmd += ' basenji_train.py'
cmd += ' %s' % options_string(options, train_options,
'%s/train' % rep_dir)
cmd += ' %s %s' % (params_file, data_dir)
name = '%s-train%d' % (options.name, pi)
sbf = os.path.abspath('%s/train.sb' % rep_dir)
outf = os.path.abspath('%s/train.out' % rep_dir)
errf = os.path.abspath('%s/train.err' % rep_dir)
j = slurm.Job(cmd,
name,
outf,
errf,
sbf,
queue=options.queue,
gpu=params_train.get('num_gpu', 1),
mem=23000,
time='28-0:0:0')
jobs.append(j)
slurm.multi_run(jobs,
max_proc=options.processes,
verbose=True,
launch_sleep=10,
update_sleep=60)
#######################################################
# test train
jobs = []
for pi in range(options.processes):
rep_dir = '%s/%d' % (options.out_dir, pi)
test_dir = '%s/test_train' % rep_dir
# check if done
acc_file = '%s/acc.txt' % test_dir
if options.restart and os.path.isfile(acc_file):
print('%s already generated.' % acc_file)
else:
cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
cmd += ' conda activate %s;' % options.conda_env
cmd += ' echo $HOSTNAME;'
cmd += ' basenji_test.py'
if options.rc:
cmd += ' --rc'
if options.shifts:
cmd += ' --shifts %s' % options.shifts
cmd += ' -o %s' % test_dir
cmd += ' --tfr "train-*.tfr"'
cmd += ' %s %s/train/model_check.h5 %s' % (params_file, rep_dir,
data_dir)
name = '%s-testtr%d' % (options.name, pi)
sbf = os.path.abspath('%s/test_train.sb' % rep_dir)
outf = os.path.abspath('%s/test_train.out' % rep_dir)
errf = os.path.abspath('%s/test_train.err' % rep_dir)
j = slurm.Job(cmd,
name,
outf,
errf,
sbf,
queue=options.queue,
gpu=params_train.get('num_gpu', 1),
mem=23000,
time='4:0:0')
jobs.append(j)
#######################################################
# test best
for pi in range(options.processes):
rep_dir = '%s/%d' % (options.out_dir, pi)
test_dir = '%s/test' % rep_dir
# check if done
acc_file = '%s/acc.txt' % test_dir
if options.restart and os.path.isfile(acc_file):
print('%s already generated.' % acc_file)
else:
cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
cmd += ' conda activate %s;' % options.conda_env
cmd += ' echo $HOSTNAME;'
cmd += ' basenji_test.py'
if options.rc:
cmd += ' --rc'
if options.shifts:
cmd += ' --shifts %s' % options.shifts
cmd += ' -o %s' % test_dir
cmd += ' %s %s/train/model_best.h5 %s' % (params_file, rep_dir,
data_dir)
name = '%s-test%d' % (options.name, pi)
sbf = os.path.abspath('%s/test.sb' % rep_dir)
outf = os.path.abspath('%s/test.out' % rep_dir)
errf = os.path.abspath('%s/test.err' % rep_dir)
j = slurm.Job(cmd,
name,
outf,
errf,
sbf,
queue=options.queue,
gpu=params_train.get('num_gpu', 1),
mem=23000,
time='4:0:0')
jobs.append(j)
#######################################################
# test best specificity
for pi in range(options.processes):
rep_dir = '%s/%d' % (options.out_dir, pi)
test_dir = '%s/test_spec' % rep_dir
# check if done
acc_file = '%s/acc.txt' % test_dir
if options.restart and os.path.isfile(acc_file):
print('%s already generated.' % acc_file)
else:
cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;'
cmd += ' conda activate %s;' % options.conda_env
cmd += ' echo $HOSTNAME;'
cmd += ' basenji_test_specificity.py'
if options.rc:
cmd += ' --rc'
if options.shifts:
cmd += ' --shifts %s' % options.shifts
cmd += ' -o %s' % test_dir
cmd += ' %s %s/train/model_best.h5 %s' % (params_file, rep_dir,
data_dir)
name = '%s-spec%d' % (options.name, pi)
sbf = os.path.abspath('%s/test_spec.sb' % rep_dir)
outf = os.path.abspath('%s/test_spec.out' % rep_dir)
errf = os.path.abspath('%s/test_spec.err' % rep_dir)
# sticking to one gpu because the normalization time dominates
# better would be to save predictions above.
j = slurm.Job(cmd,
name,
outf,
errf,
sbf,
queue=options.queue,
gpu=1,
mem=45000,
time='8:0:0')
jobs.append(j)
slurm.multi_run(jobs,
max_proc=options.processes,
verbose=True,
launch_sleep=10,
update_sleep=60)
def main():
usage = 'usage: %prog [options] <params_file> <model_file> <genes_hdf5_file> <vcf_file>'
parser = OptionParser(usage)
parser.add_option(
'-a',
dest='all_sed',
default=False,
action='store_true',
help=
'Print all variant-gene pairs, as opposed to only nonzero [Default: %default]'
)
parser.add_option('-b',
dest='batch_size',
default=None,
type='int',
help='Batch size [Default: %default]')
parser.add_option('-c',
dest='csv',
default=False,
action='store_true',
help='Print table as CSV [Default: %default]')
parser.add_option('-g',
dest='genome_file',
default='%s/assembly/human.hg19.genome' %
os.environ['HG19'],
help='Chromosome lengths file [Default: %default]')
parser.add_option(
'-i',
dest='index_snp',
default=False,
action='store_true',
help=
'SNPs are labeled with their index SNP as column 6 [Default: %default]'
)
parser.add_option(
'-o',
dest='out_dir',
default='sed',
help='Output directory for tables and plots [Default: %default]')
parser.add_option(
'-p',
dest='processes',
default=2,
type='int',
help='Number of parallel processes to run [Default: %default]')
parser.add_option(
'-q',
dest='queue',
default='p100',
help='SLURM queue on which to run the jobs [Default: %default]')
parser.add_option(
'--rc',
dest='rc',
default=False,
action='store_true',
help=
'Average the forward and reverse complement predictions when testing [Default: %default]'
)
parser.add_option(
'-s',
dest='score',
default=False,
action='store_true',
help='SNPs are labeled with scores as column 7 [Default: %default]')
parser.add_option(
'-t',
dest='target_wigs_file',
default=None,
help='Store target values, extracted from this list of WIG files')
parser.add_option(
'--ti',
dest='track_indexes',
help='Comma-separated list of target indexes to output BigWig tracks')
parser.add_option(
'-x',
dest='transcript_table',
default=False,
action='store_true',
help='Print transcript table in addition to gene [Default: %default]')
parser.add_option(
'-w',
dest='tss_width',
default=1,
type='int',
help=
'Width of bins considered to quantify TSS transcription [Default: %default]'
)
(options, args) = parser.parse_args()
if len(args) != 4:
parser.error(
'Must provide parameters and model files, genes HDF5 file, and QTL VCF file'
)
else:
params_file = args[0]
model_file = args[1]
genes_hdf5_file = args[2]
vcf_file = args[3]
#######################################################
# prep work
# output directory
if os.path.isdir(options.out_dir):
shutil.rmtree(options.out_dir)
os.mkdir(options.out_dir)
# pickle options
options_pkl_file = '%s/options.pkl' % options.out_dir
options_pkl = open(options_pkl_file, 'wb')
pickle.dump(options, options_pkl)
options_pkl.close()
#######################################################
# launch worker threads
jobs = []
for pi in range(options.processes):
cmd = 'source activate py3_gpu; basenji_sed.py %s %s %d' % (
options_pkl_file, ' '.join(args), pi)
name = 'sed_p%d' % pi
outf = '%s/job%d.out' % (options.out_dir, pi)
errf = '%s/job%d.err' % (options.out_dir, pi)
j = slurm.Job(cmd,
name,
outf,
errf,
queue=options.queue,
mem=16000,
time='4:0:0',
gpu=1)
jobs.append(j)
slurm.multi_run(jobs,
max_proc=options.processes,
verbose=True,
sleep_time=60)
#######################################################
# collect output
collect_table_multi('sed_gene.txt', options.out_dir, options.processes)
if options.transcript_table:
collect_table('sed_tx.txt', options.out_dir, options.processes)
if options.track_indexes is not None:
if not os.path.isdir('%s/tracks' % options.out_dir):
os.mkdir('%s/tracks' % options.out_dir)
for track_file in glob.glob('%s/job*/tracks/*'):
track_base = os.path.split(track_file)[1]
os.rename(track_file,
'%s/tracks/%s' % (options.out_dir, track_base))
for pi in range(options.processes):
shutil.rmtree('%s/job%d' % (options.out_dir, pi))
def main():
usage = 'usage: %prog [options] <fasta_file> <targets_file>'
parser = OptionParser(usage)
parser.add_option('-b',
dest='blacklist_bed',
help='Set blacklist nucleotides to a baseline value.')
parser.add_option(
'--break',
dest='break_t',
default=786432,
type='int',
help='Break in half contigs above length [Default: %default]')
parser.add_option('-c',
'--crop',
dest='crop_bp',
default=0,
type='int',
help='Crop bp off each end [Default: %default]')
parser.add_option('-d',
dest='sample_pct',
default=1.0,
type='float',
help='Down-sample the segments')
parser.add_option('-f',
dest='folds',
default=None,
type='int',
help='Generate cross fold split [Default: %default]')
parser.add_option('-g',
dest='gaps_file',
help='Genome assembly gaps BED [Default: %default]')
parser.add_option('-i',
dest='interp_nan',
default=False,
action='store_true',
help='Interpolate NaNs [Default: %default]')
parser.add_option('-l',
dest='seq_length',
default=131072,
type='int',
help='Sequence length [Default: %default]')
parser.add_option(
'--limit',
dest='limit_bed',
help='Limit to segments that overlap regions in a BED file')
parser.add_option(
'--local',
dest='run_local',
default=False,
action='store_true',
help='Run jobs locally as opposed to on SLURM [Default: %default]')
parser.add_option('-o',
dest='out_dir',
default='data_out',
help='Output directory [Default: %default]')
parser.add_option('-p',
dest='processes',
default=None,
type='int',
help='Number parallel processes [Default: %default]')
parser.add_option(
'--peaks',
dest='peaks_only',
default=False,
action='store_true',
help='Create contigs only from peaks [Default: %default]')
parser.add_option('-r',
dest='seqs_per_tfr',
default=256,
type='int',
help='Sequences per TFRecord file [Default: %default]')
parser.add_option(
'--restart',
dest='restart',
default=False,
action='store_true',
help='Continue progress from midpoint. [Default: %default]')
parser.add_option('--seed',
dest='seed',
default=44,
type='int',
help='Random seed [Default: %default]')
parser.add_option(
'--snap',
dest='snap',
default=1,
type='int',
help='Snap sequences to multiple of the given value [Default: %default]'
)
parser.add_option('--st',
'--split_test',
dest='split_test',
default=False,
action='store_true',
help='Exit after split. [Default: %default]')
parser.add_option(
'--stride',
'--stride_train',
dest='stride_train',
default=1.,
type='float',
help='Stride to advance train sequences [Default: seq_length]')
parser.add_option(
'--stride_test',
dest='stride_test',
default=1.,
type='float',
help='Stride to advance valid and test sequences [Default: seq_length]'
)
parser.add_option(
'-t',
dest='test_pct_or_chr',
default=0.05,
type='str',
help='Proportion of the data for testing [Default: %default]')
parser.add_option('-u',
dest='umap_bed',
help='Unmappable regions in BED format')
parser.add_option(
'--umap_t',
dest='umap_t',
default=0.5,
type='float',
help=
'Remove sequences with more than this unmappable bin % [Default: %default]'
)
parser.add_option(
'--umap_clip',
dest='umap_clip',
default=1,
type='float',
help=
'Clip values at unmappable positions to distribution quantiles, eg 0.25. [Default: %default]'
)
parser.add_option(
'--umap_tfr',
dest='umap_tfr',
default=False,
action='store_true',
help='Save umap array into TFRecords [Default: %default]')
parser.add_option('-w',
dest='pool_width',
default=128,
type='int',
help='Sum pool width [Default: %default]')
parser.add_option(
'-v',
dest='valid_pct_or_chr',
default=0.05,
type='str',
help='Proportion of the data for validation [Default: %default]')
parser.add_option('--norm',
dest='norm',
default='',
type='str',
help='Normalize coverage values')
parser.add_option('--step',
dest='step',
default=0,
type='int',
help='Stride using bp size [Default: %pool_window]')
parser.add_option('--padding',
dest='padding',
default='valid',
type='str',
help='Padding method for sliding window approach')
(options, args) = parser.parse_args()
if len(args) != 2:
parser.error(
'Must provide FASTA and sample coverage labels and paths.')
else:
fasta_file = args[0]
targets_file = args[1]
random.seed(options.seed)
np.random.seed(options.seed)
if options.break_t is not None and options.break_t < options.seq_length:
print(
'Maximum contig length --break cannot be less than sequence length.',
file=sys.stderr)
exit(1)
# transform proportion strides to base pairs
if options.stride_train <= 1:
print('stride_train %.f' % options.stride_train, end='')
options.stride_train = options.stride_train * options.seq_length
print(' converted to %f' % options.stride_train)
options.stride_train = int(np.round(options.stride_train))
if options.stride_test <= 1:
if options.folds is None:
print('stride_test %.f' % options.stride_test, end='')
options.stride_test = options.stride_test * options.seq_length
print(' converted to %f' % options.stride_test)
options.stride_test = int(np.round(options.stride_test))
# check snap
if options.snap is not None:
if np.mod(options.seq_length, options.snap) != 0:
raise ValueError('seq_length must be a multiple of snap')
if np.mod(options.stride_train, options.snap) != 0:
raise ValueError('stride_train must be a multiple of snap')
if np.mod(options.stride_test, options.snap) != 0:
raise ValueError('stride_test must be a multiple of snap')
# setup output directory
if os.path.isdir(options.out_dir) and not options.restart:
print('Remove output directory %s or use --restart option.' %
options.out_dir)
exit(1)
elif not os.path.isdir(options.out_dir):
os.mkdir(options.out_dir)
# read target datasets
targets_df = pd.read_csv(targets_file, index_col=0, sep='\t')
################################################################
# define genomic contigs
################################################################
if not options.restart:
chrom_contigs = genome.load_chromosomes(fasta_file)
# remove gaps
if options.gaps_file:
chrom_contigs = genome.split_contigs(chrom_contigs,
options.gaps_file)
# ditch the chromosomes for contigs
contigs = []
for chrom in chrom_contigs:
if len(chrom.split('_')) == 1 and chrom != 'chrM':
contigs += [
Contig(chrom, ctg_start, ctg_end)
for ctg_start, ctg_end in chrom_contigs[chrom]
]
# limit to a BED file
if options.limit_bed is not None:
contigs = limit_contigs(contigs, options.limit_bed)
# limit to peaks
if options.peaks_only:
peaks_bed = curate_peaks(targets_df, options.out_dir,
options.pool_width, options.crop_bp)
contigs = limit_contigs(contigs, peaks_bed)
# filter for large enough
contigs = [
ctg for ctg in contigs if ctg.end - ctg.start >= options.seq_length
]
# break up large contigs
if options.break_t is not None:
contigs = break_large_contigs(contigs, options.break_t)
# print contigs to BED file
# ctg_bed_file = '%s/contigs.bed' % options.out_dir
# write_seqs_bed(ctg_bed_file, contigs)
################################################################
# divide between train/valid/test
################################################################
# label folds
if options.folds is not None:
fold_labels = ['fold%d' % fi for fi in range(options.folds)]
num_folds = options.folds
else:
fold_labels = ['train', 'valid', 'test']
num_folds = 3
if not options.restart:
if options.folds is not None:
# divide by fold pct
fold_contigs = divide_contigs_folds(contigs, options.folds)
else:
try:
# convert to float pct
valid_pct = float(options.valid_pct_or_chr)
test_pct = float(options.test_pct_or_chr)
assert (0 <= valid_pct <= 1)
assert (0 <= test_pct <= 1)
# divide by pct
fold_contigs = divide_contigs_pct(contigs, test_pct, valid_pct)
except (ValueError, AssertionError):
# divide by chr
valid_chrs = options.valid_pct_or_chr.split(',')
test_chrs = options.test_pct_or_chr.split(',')
fold_contigs = divide_contigs_chr(contigs, test_chrs,
valid_chrs)
# rejoin broken contigs within set
for fi in range(len(fold_contigs)):
fold_contigs[fi] = rejoin_large_contigs(fold_contigs[fi])
# write labeled contigs to BED file
ctg_bed_file = '%s/contigs.bed' % options.out_dir
ctg_bed_out = open(ctg_bed_file, 'w')
for fi in range(len(fold_contigs)):
for ctg in fold_contigs[fi]:
line = '%s\t%d\t%d\t%s' % (ctg.chr, ctg.start, ctg.end,
fold_labels[fi])
print(line, file=ctg_bed_out)
ctg_bed_out.close()
if options.split_test:
exit()
################################################################
# define model sequences
################################################################
if not options.restart:
fold_mseqs = []
for fi in range(num_folds):
if fold_labels[fi] in ['valid', 'test']:
stride_fold = options.stride_test
else:
stride_fold = options.stride_train
# stride sequences across contig
fold_mseqs_fi = contig_sequences(fold_contigs[fi],
options.seq_length, stride_fold,
options.snap, fold_labels[fi])
fold_mseqs.append(fold_mseqs_fi)
# shuffle
random.shuffle(fold_mseqs[fi])
# down-sample
if options.sample_pct < 1.0:
fold_mseqs[fi] = random.sample(
fold_mseqs[fi],
int(options.sample_pct * len(fold_mseqs[fi])))
# merge into one list
mseqs = [ms for fm in fold_mseqs for ms in fm]
################################################################
# mappability
################################################################
if not options.restart:
if options.umap_bed is not None:
if shutil.which('bedtools') is None:
print('Install Bedtools to annotate unmappable sites',
file=sys.stderr)
exit(1)
# annotate unmappable positions
mseqs_unmap = annotate_unmap(mseqs, options.umap_bed,
options.seq_length,
options.pool_width, options.crop_bp)
# filter unmappable
mseqs_map_mask = (mseqs_unmap.mean(axis=1, dtype='float64') <
options.umap_t)
mseqs = [mseqs[i] for i in range(len(mseqs)) if mseqs_map_mask[i]]
mseqs_unmap = mseqs_unmap[mseqs_map_mask, :]
# write to file
unmap_npy = '%s/mseqs_unmap.npy' % options.out_dir
np.save(unmap_npy, mseqs_unmap)
# write sequences to BED
seqs_bed_file = '%s/sequences.bed' % options.out_dir
write_seqs_bed(seqs_bed_file, mseqs, True)
else:
# read from directory
seqs_bed_file = '%s/sequences.bed' % options.out_dir
unmap_npy = '%s/mseqs_unmap.npy' % options.out_dir
mseqs = []
fold_mseqs = []
for fi in range(num_folds):
fold_mseqs.append([])
for line in open(seqs_bed_file):
a = line.split()
msg = ModelSeq(a[0], int(a[1]), int(a[2]), a[3])
mseqs.append(msg)
if a[3] == 'train':
fi = 0
elif a[3] == 'valid':
fi = 1
elif a[3] == 'test':
fi = 2
else:
fi = int(a[3].replace('fold', ''))
fold_mseqs[fi].append(msg)
################################################################
# read sequence coverage values
################################################################
seqs_cov_dir = '%s/seqs_cov' % options.out_dir
if not os.path.isdir(seqs_cov_dir):
os.mkdir(seqs_cov_dir)
read_jobs = []
for ti in range(targets_df.shape[0]):
genome_cov_file = targets_df['file'].iloc[ti]
seqs_cov_stem = '%s/%d' % (seqs_cov_dir, ti)
seqs_cov_file = '%s.h5' % seqs_cov_stem
clip_ti = None
if 'clip' in targets_df.columns:
clip_ti = targets_df['clip'].iloc[ti]
clipsoft_ti = None
if 'clip_soft' in targets_df.columns:
clipsoft_ti = targets_df['clip_soft'].iloc[ti]
scale_ti = 1
if 'scale' in targets_df.columns:
scale_ti = targets_df['scale'].iloc[ti]
if options.restart and os.path.isfile(seqs_cov_file):
print('Skipping existing %s' % seqs_cov_file, file=sys.stderr)
else:
cmd = '/home/shush/profile/tfprofile/bin/basenji_data_read.py'
cmd += ' --crop %d' % options.crop_bp
cmd += ' -w %d' % options.pool_width
cmd += ' -u %s' % targets_df['sum_stat'].iloc[ti]
if clip_ti is not None:
cmd += ' -c %f' % clip_ti
if clipsoft_ti is not None:
cmd += ' --clip_soft %f' % clipsoft_ti
cmd += ' -s %f' % scale_ti
if options.blacklist_bed:
cmd += ' -b %s' % options.blacklist_bed
if options.interp_nan:
cmd += ' -i'
if options.norm:
cmd += ' --norm %s' % options.norm
if options.step:
cmd += ' --step %i' % options.step
if options.padding:
cmd += ' --padding %s' % options.padding
cmd += ' %s' % genome_cov_file
cmd += ' %s' % seqs_bed_file
cmd += ' %s' % seqs_cov_file
if options.run_local:
# breaks on some OS
# cmd += ' &> %s.err' % seqs_cov_stem
read_jobs.append(cmd)
else:
j = slurm.Job(cmd,
name='read_t%d' % ti,
out_file='%s.out' % seqs_cov_stem,
err_file='%s.err' % seqs_cov_stem,
queue='standard',
mem=15000,
time='12:0:0')
read_jobs.append(j)
if options.run_local:
util.exec_par(read_jobs, options.processes, verbose=True)
else:
slurm.multi_run(read_jobs,
options.processes,
verbose=True,
launch_sleep=1,
update_sleep=5)
################################################################
# write TF Records
################################################################
# copy targets file
shutil.copy(targets_file, '%s/targets.txt' % options.out_dir)
# initialize TF Records dir
tfr_dir = '%s/tfrecords' % options.out_dir
if not os.path.isdir(tfr_dir):
os.mkdir(tfr_dir)
write_jobs = []
for fold_set in fold_labels:
fold_set_indexes = [
i for i in range(len(mseqs)) if mseqs[i].label == fold_set
]
fold_set_start = fold_set_indexes[0]
fold_set_end = fold_set_indexes[-1] + 1
tfr_i = 0
tfr_start = fold_set_start
tfr_end = min(tfr_start + options.seqs_per_tfr, fold_set_end)
while tfr_start <= fold_set_end:
tfr_stem = '%s/%s-%d' % (tfr_dir, fold_set, tfr_i)
cmd = '/home/shush/profile/tfprofile/bin/basenji_data_write.py'
cmd += ' -s %d' % tfr_start
cmd += ' -e %d' % tfr_end
cmd += ' --umap_clip %f' % options.umap_clip
if options.umap_tfr:
cmd += ' --umap_tfr'
if options.umap_bed is not None:
cmd += ' -u %s' % unmap_npy
cmd += ' %s' % fasta_file
cmd += ' %s' % seqs_bed_file
cmd += ' %s' % seqs_cov_dir
cmd += ' %s.tfr' % tfr_stem
if options.run_local:
# breaks on some OS
# cmd += ' &> %s.err' % tfr_stem
write_jobs.append(cmd)
else:
j = slurm.Job(cmd,
name='write_%s-%d' % (fold_set, tfr_i),
out_file='%s.out' % tfr_stem,
err_file='%s.err' % tfr_stem,
queue='standard',
mem=15000,
time='12:0:0')
write_jobs.append(j)
# update
tfr_i += 1
tfr_start += options.seqs_per_tfr
tfr_end = min(tfr_start + options.seqs_per_tfr, fold_set_end)
if options.run_local:
util.exec_par(write_jobs, options.processes, verbose=True)
else:
slurm.multi_run(write_jobs,
options.processes,
verbose=True,
launch_sleep=1,
update_sleep=5)
################################################################
# stats
################################################################
stats_dict = {}
stats_dict['num_targets'] = targets_df.shape[0]
stats_dict['seq_length'] = options.seq_length
stats_dict['pool_width'] = options.pool_width
stats_dict['crop_bp'] = options.crop_bp
target_length = options.seq_length - 2 * options.crop_bp
target_length = target_length // options.pool_width
stats_dict['target_length'] = target_length
for fi in range(num_folds):
stats_dict['%s_seqs' % fold_labels[fi]] = len(fold_mseqs[fi])
for i in range(10):
print('~~~')
print('%s/statistics.json' % options.out_dir)
for i in range(10):
print('~~~')
with open('%s/statistics.json' % options.out_dir, 'w') as stats_json_out:
json.dump(stats_dict, stats_json_out, indent=4)
def main():
usage = 'usage: %prog [options] <params_file> <model_file> <vcf_file>'
parser = OptionParser(usage)
parser.add_option('-b',
dest='batch_size',
default=256,
type='int',
help='Batch size [Default: %default]')
parser.add_option('-c',
dest='csv',
default=False,
action='store_true',
help='Print table as CSV [Default: %default]')
parser.add_option(
'-e',
dest='heatmaps',
default=False,
action='store_true',
help='Draw score heatmaps, grouped by index SNP [Default: %default]')
parser.add_option(
'-f',
dest='genome_fasta',
default='%s/assembly/hg19.fa' % os.environ['HG19'],
help=
'Genome FASTA from which sequences will be drawn [Default: %default]')
parser.add_option('-g',
dest='genome_file',
default='%s/assembly/human.hg19.genome' %
os.environ['HG19'],
help='Chromosome lengths file [Default: %default]')
parser.add_option(
'-l',
dest='seq_len',
type='int',
default=131072,
help='Sequence length provided to the model [Default: %default]')
parser.add_option('--local',
dest='local',
default=1024,
type='int',
help='Local SAD score [Default: %default]')
parser.add_option('-n',
dest='norm_file',
default=None,
help='Normalize SAD scores')
parser.add_option(
'-o',
dest='out_dir',
default='sad',
help='Output directory for tables and plots [Default: %default]')
parser.add_option('-p',
dest='processes',
default=2,
type='int',
help='Number of parallel processes to run.')
parser.add_option('--pseudo',
dest='log_pseudo',
default=1,
type='float',
help='Log2 pseudocount [Default: %default]')
parser.add_option(
'-q',
dest='queue',
default='p100',
help='SLURM queue on which to run the jobs [Default: %default]')
parser.add_option(
'--rc',
dest='rc',
default=False,
action='store_true',
help=
'Average the forward and reverse complement predictions when testing [Default: %default]'
)
parser.add_option('--shifts',
dest='shifts',
default='0',
help='Ensemble prediction shifts [Default: %default]')
parser.add_option(
'-t',
dest='targets_file',
default=None,
help='File specifying target indexes and labels in table format')
parser.add_option(
'--ti',
dest='track_indexes',
help='Comma-separated list of target indexes to output BigWig tracks')
parser.add_option(
'-u',
dest='penultimate',
default=False,
action='store_true',
help='Compute SED in the penultimate layer [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 3:
parser.error('Must provide parameters and model files and VCF file')
else:
params_file = args[0]
model_file = args[1]
vcf_file = args[2]
#######################################################
# prep work
# output directory
if os.path.isdir(options.out_dir):
shutil.rmtree(options.out_dir)
os.mkdir(options.out_dir)
# pickle options
options_pkl_file = '%s/options.pkl' % options.out_dir
options_pkl = open(options_pkl_file, 'wb')
pickle.dump(options, options_pkl)
options_pkl.close()
#######################################################
# launch worker threads
jobs = []
for pi in range(options.processes):
cmd = 'source activate py3_gpu; basenji_sad.py %s %s %d' % (
options_pkl_file, ' '.join(args), pi)
name = 'sad_p%d' % pi
outf = '%s/job%d.out' % (options.out_dir, pi)
errf = '%s/job%d.err' % (options.out_dir, pi)
j = slurm.Job(cmd,
name,
outf,
errf,
queue=options.queue,
mem=15000,
time='7-0:0:0',
gpu=1)
jobs.append(j)
slurm.multi_run(jobs,
max_proc=options.processes,
verbose=True,
sleep_time=60)
#######################################################
# collect output
collect_table('sad_table.txt', options.out_dir, options.processes)