def main():
usage = 'usage: %prog [options] <model_th> <vcf_file>'
parser = OptionParser(usage)
parser.add_option('-c', dest='csv', default=False, action='store_true', help='Print table as CSV [Default: %default]')
parser.add_option('--cuda', dest='cuda', default=False, action='store_true', help='Predict on the GPU [Default: %default]')
parser.add_option('--cudnn', dest='cudnn', default=False, action='store_true', help='Predict on the GPU w/ CuDNN [Default: %default]')
parser.add_option('-d', dest='model_hdf5_file', default=None, help='Pre-computed model output as HDF5 [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/data/genomes/hg19.fa'%os.environ['BASSETDIR'], help='Genome FASTA from which sequences will be drawn [Default: %default]')
parser.add_option('--f1', dest='genome1_fasta', default=None, help='Genome FASTA which which major allele sequences will be drawn')
parser.add_option('--f2', dest='genome2_fasta', default=None, help='Genome FASTA which which minor allele sequences will be drawn')
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('-l', dest='seq_len', type='int', default=600, help='Sequence length provided to the model [Default: %default]')
parser.add_option('-m', dest='min_limit', default=0.1, type='float', help='Minimum heatmap limit [Default: %default]')
parser.add_option('-o', dest='out_dir', default='sad', help='Output directory for tables and plots [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='targets_file', default=None, help='File specifying target indexes and labels in table format')
(options,args) = parser.parse_args()
if len(args) != 2:
parser.error('Must provide Torch model and VCF file')
else:
model_th = args[0]
vcf_file = args[1]
if not os.path.isdir(options.out_dir):
os.mkdir(options.out_dir)
#################################################################
# prep SNP sequences
#################################################################
# load SNPs
snps = vcf.vcf_snps(vcf_file, options.index_snp, options.score, options.genome2_fasta is not None)
# get one hot coded input sequences
if not options.genome1_fasta or not options.genome2_fasta:
seq_vecs, seqs, seq_headers, snps = vcf.snps_seq1(snps, options.seq_len, options.genome_fasta)
else:
seq_vecs, seqs, seq_headers, snps = vcf.snps2_seq1(snps, options.seq_len, options.genome1_fasta, options.genome2_fasta)
# reshape sequences for torch
seq_vecs = seq_vecs.reshape((seq_vecs.shape[0],4,1,seq_vecs.shape[1]/4))
# write to HDF5
h5f = h5py.File('%s/model_in.h5'%options.out_dir, 'w')
h5f.create_dataset('test_in', data=seq_vecs)
h5f.close()
#################################################################
# predict in Torch
#################################################################
if options.model_hdf5_file is None:
if options.cudnn:
cuda_str = '-cudnn'
elif options.cuda:
cuda_str = '-cuda'
else:
cuda_str = ''
options.model_hdf5_file = '%s/model_out.txt' % options.out_dir
cmd = 'basset_predict.lua -rc %s %s %s/model_in.h5 %s' % (cuda_str, model_th, options.out_dir, options.model_hdf5_file)
print cmd
subprocess.call(cmd, shell=True)
# read in predictions
seq_preds = []
for line in open(options.model_hdf5_file):
seq_preds.append(np.array([np.float16(p) for p in line.split()]))
seq_preds = np.array(seq_preds)
#################################################################
# collect and print SADs
#################################################################
if options.targets_file is None:
target_labels = ['t%d' % ti for ti in range(seq_preds.shape[1])]
else:
target_labels = [line.split()[0] for line in open(options.targets_file)]
header_cols = ('rsid', 'index', 'score', 'ref', 'alt', 'target', 'ref_pred', 'alt pred', 'sad')
if options.csv:
sad_out = open('%s/sad_table.csv' % options.out_dir, 'w')
print >> sad_out, ','.join(header_cols)
else:
sad_out = open('%s/sad_table.txt' % options.out_dir, 'w')
print >> sad_out, ' '.join(header_cols)
# hash by index snp
sad_matrices = {}
sad_labels = {}
sad_scores = {}
pi = 0
for snp in snps:
# get reference prediction
ref_preds = seq_preds[pi,:]
pi += 1
for alt_al in snp.alt_alleles:
# get alternate prediction
alt_preds = seq_preds[pi,:]
pi += 1
# normalize by reference
alt_sad = alt_preds - ref_preds
sad_matrices.setdefault(snp.index_snp,[]).append(alt_sad)
# label as mutation from reference
alt_label = '%s_%s>%s' % (snp.rsid, vcf.cap_allele(snp.ref_allele), vcf.cap_allele(alt_al))
sad_labels.setdefault(snp.index_snp,[]).append(alt_label)
# save scores
sad_scores.setdefault(snp.index_snp,[]).append(snp.score)
# print table lines
for ti in range(len(alt_sad)):
if options.index_snp and options.score:
cols = (snp.rsid, snp.index_snp, snp.score, vcf.cap_allele(snp.ref_allele), vcf.cap_allele(alt_al), target_labels[ti], ref_preds[ti], alt_preds[ti], alt_sad[ti])
if options.csv:
print >> sad_out, ','.join([str(c) for c in cols])
else:
print >> sad_out, '%-13s %-13s %5.3f %6s %6s %12s %6.4f %6.4f %7.4f' % cols
elif options.index_snp:
cols = (snp.rsid, snp.index_snp, vcf.cap_allele(snp.ref_allele), vcf.cap_allele(alt_al), target_labels[ti], ref_preds[ti], alt_preds[ti], alt_sad[ti])
if options.csv:
print >> sad_out, ','.join([str(c) for c in cols])
else:
print >> sad_out, '%-13s %-13s %6s %6s %12s %6.4f %6.4f %7.4f' % cols
elif options.score:
cols = (snp.rsid, snp.score, vcf.cap_allele(snp.ref_allele), vcf.cap_allele(alt_al), target_labels[ti], ref_preds[ti], alt_preds[ti], alt_sad[ti])
if options.csv:
print >> sad_out, ','.join([str(c) for c in cols])
else:
print >> sad_out, '%-13s %5.3f %6s %6s %12s %6.4f %6.4f %7.4f' % cols
else:
cols = (snp.rsid, vcf.cap_allele(snp.ref_allele), vcf.cap_allele(alt_al), target_labels[ti], ref_preds[ti], alt_preds[ti], alt_sad[ti])
if options.csv:
print >> sad_out, ','.join([str(c) for c in cols])
else:
print >> sad_out, '%-13s %6s %6s %12s %6.4f %6.4f %7.4f' % cols
sad_out.close()
#################################################################
# plot SAD heatmaps
#################################################################
if options.heatmaps:
for ii in sad_matrices:
# convert fully to numpy arrays
sad_matrix = abs(np.array(sad_matrices[ii]))
print ii, sad_matrix.shape
if sad_matrix.shape[0] > 1:
vlim = max(options.min_limit, sad_matrix.max())
score_mat = np.reshape(np.array(sad_scores[ii]), (-1, 1))
# plot heatmap
plt.figure(figsize=(20, 0.5 + 0.5*sad_matrix.shape[0]))
if options.score:
# lay out scores
cols = 12
ax_score = plt.subplot2grid((1,cols), (0,0))
ax_sad = plt.subplot2grid((1,cols), (0,1), colspan=(cols-1))
sns.heatmap(score_mat, xticklabels=False, yticklabels=False, vmin=0, vmax=1, cmap='Reds', cbar=False, ax=ax_score)
else:
ax_sad = plt.gca()
sns.heatmap(sad_matrix, xticklabels=target_labels, yticklabels=sad_labels[ii], vmin=0, vmax=vlim, ax=ax_sad)
for tick in ax_sad.get_xticklabels():
tick.set_rotation(-45)
tick.set_horizontalalignment('left')
tick.set_fontsize(5)
plt.tight_layout()
if ii == '.':
out_pdf = '%s/sad_heat.pdf' % options.out_dir
else:
out_pdf = '%s/sad_%s_heat.pdf' % (options.out_dir, ii)
plt.savefig(out_pdf)
plt.close()
def main():
usage = 'usage: %prog [options] <model_file> <vcf_file>'
parser = OptionParser(usage)
parser.add_option('-d', dest='model_hdf5_file', default=None, help='Pre-computed model output as HDF5 [Default: %default]')
parser.add_option('-f', dest='genome_fasta', default='%s/data/genomes/hg19.fa'%os.environ['BASSETDIR'], help='Genome FASTA from which sequences will be drawn [Default: %default]')
parser.add_option('-g', dest='gain_height', default=False, action='store_true', help='Nucleotide heights determined by the max of loss and gain [Default: %default]')
parser.add_option('-l', dest='seq_len', type='int', default=600, help='Sequence length provided to the model [Default: %default]')
parser.add_option('-m', dest='min_limit', default=0.1, type='float', help='Minimum heatmap limit [Default: %default]')
parser.add_option('-n', dest='center_nt', default=200, type='int', help='Nt around the SNP to mutate and plot in the heatmap [Default: %default]')
parser.add_option('-o', dest='out_dir', default='heat', help='Output directory [Default: %default]')
parser.add_option('-t', dest='targets', default='0', help='Comma-separated list of target indexes to plot (or -1 for all) [Default: %default]')
(options,args) = parser.parse_args()
if len(args) != 2:
parser.error('Must provide Basset model file and input SNPs in VCF format')
else:
model_file = args[0]
vcf_file = args[1]
if not os.path.isdir(options.out_dir):
os.mkdir(options.out_dir)
#################################################################
# prep SNP sequences
#################################################################
# load SNPs
snps = vcf.vcf_snps(vcf_file)
# get one hot coded input sequences
seqs_1hot, seqs, seq_headers = vcf.snps_seq1(snps, options.genome_fasta, options.seq_len)
# reshape sequences for torch
seqs_1hot = seqs_1hot.reshape((seqs_1hot.shape[0],4,1,seqs_1hot.shape[1]/4))
# write to HDF5
model_input_hdf5 = '%s/model_in.h5'%options.out_dir
h5f = h5py.File(model_input_hdf5, 'w')
h5f.create_dataset('test_in', data=seqs_1hot)
h5f.close()
#################################################################
# Torch predict modifications
#################################################################
if options.model_hdf5_file is None:
options.model_hdf5_file = '%s/model_out.h5' % options.out_dir
torch_cmd = 'basset_sat_predict.lua -center_nt %d %s %s %s' % (options.center_nt, model_file, model_input_hdf5, options.model_hdf5_file)
if subprocess.call(torch_cmd, shell=True):
message('Error running basset_sat_predict.lua', 'error')
#################################################################
# load modification predictions
#################################################################
hdf5_in = h5py.File(options.model_hdf5_file, 'r')
seq_mod_preds = np.array(hdf5_in['seq_mod_preds'])
hdf5_in.close()
# trim seqs to match seq_mod_preds length
delta_start = 0
delta_len = seq_mod_preds.shape[2]
if delta_len < options.seq_len:
delta_start = (options.seq_len - delta_len)/2
for si in range(len(seqs)):
seqs[si] = seqs[si][delta_start:delta_start+delta_len]
# decide which cells to plot
if options.targets == '-1':
plot_cells = xrange(seq_mod_preds.shape[3])
else:
plot_cells = [int(ci) for ci in options.targets.split(',')]
#################################################################
# plot
#################################################################
table_out = open('%s/table.txt' % options.out_dir, 'w')
rdbu = sns.color_palette("RdBu_r", 10)
nts = 'ACGT'
for si in range(seq_mod_preds.shape[0]):
header = seq_headers[si]
seq = seqs[si]
# plot some descriptive heatmaps for each individual cell type
for ci in plot_cells:
seq_mod_preds_cell = seq_mod_preds[si,:,:,ci]
real_pred_cell = get_real_pred(seq_mod_preds_cell, seq)
# compute matrices
norm_matrix = seq_mod_preds_cell - real_pred_cell
min_scores = seq_mod_preds_cell.min(axis=0)
max_scores = seq_mod_preds_cell.max(axis=0)
minmax_matrix = np.vstack([min_scores - real_pred_cell, max_scores - real_pred_cell])
# prepare figure
sns.set(style='white', font_scale=0.5)
sns.axes_style({'axes.linewidth':1})
heat_cols = 400
sad_start = 1
sad_end = 323
logo_start = 0
logo_end = 324
fig = plt.figure(figsize=(20,3))
ax_logo = plt.subplot2grid((3,heat_cols), (0,logo_start), colspan=(logo_end-logo_start))
ax_sad = plt.subplot2grid((3,heat_cols), (1,sad_start), colspan=(sad_end-sad_start))
ax_heat = plt.subplot2grid((3,heat_cols), (2,0), colspan=heat_cols)
# print a WebLogo of the sequence
vlim = max(options.min_limit, abs(minmax_matrix).max())
if options.gain_height:
seq_heights = 0.25 + 1.75/vlim*(abs(minmax_matrix).max(axis=0))
else:
seq_heights = 0.25 + 1.75/vlim*(-minmax_matrix[0])
logo_eps = '%s/%s_c%d_seq.eps' % (options.out_dir, header.replace(':','_'), ci)
seq_logo(seq, seq_heights, logo_eps)
# add to figure
logo_png = '%s.png' % logo_eps[:-4]
logo_cmd = 'convert -density 300 %s %s' % (logo_eps, logo_png)
if subprocess.call(logo_cmd, shell=True):
message('Error running convert', 'error')
logo = Image.open(logo_png)
ax_logo.imshow(logo)
ax_logo.set_axis_off()
# plot loss and gain SAD scores
ax_sad.plot(-minmax_matrix[0], c=rdbu[0], label='loss', linewidth=1)
ax_sad.plot(minmax_matrix[1], c=rdbu[-1], label='gain', linewidth=1)
ax_sad.set_xlim(0,minmax_matrix.shape[1])
ax_sad.legend()
# ax_sad.grid(True, linestyle=':')
for axis in ['top','bottom','left','right']:
ax_sad.spines[axis].set_linewidth(0.5)
# plot real-normalized scores
vlim = max(options.min_limit, abs(norm_matrix).max())
sns.heatmap(norm_matrix, linewidths=0, cmap='RdBu_r', vmin=-vlim, vmax=vlim, xticklabels=False, ax=ax_heat)
ax_heat.yaxis.set_ticklabels('TGCA', rotation='horizontal') # , size=10)
# save final figure
plt.tight_layout()
plt.savefig('%s/%s_c%d_heat.pdf' % (options.out_dir,header.replace(':','_'), ci), dpi=300)
plt.close()
#################################################################
# print table of nt variability for each cell
#################################################################
for ci in range(seq_mod_preds.shape[3]):
seq_mod_preds_cell = seq_mod_preds[si,:,:,ci]
real_pred_cell = get_real_pred(seq_mod_preds_cell, seq)
min_scores = seq_mod_preds_cell.min(axis=0)
max_scores = seq_mod_preds_cell.max(axis=0)
loss_matrix = real_pred_cell - seq_mod_preds_cell.min(axis=0)
gain_matrix = seq_mod_preds_cell.max(axis=0) - real_pred_cell
for pos in range(seq_mod_preds_cell.shape[1]):
cols = [header, delta_start+pos, ci, loss_matrix[pos], gain_matrix[pos]]
print >> table_out, '\t'.join([str(c) for c in cols])
table_out.close()
def main():
usage = 'usage: %prog [options] <model_th> <vcf_file>'
parser = OptionParser(usage)
parser.add_option('-c',
dest='csv',
default=False,
action='store_true',
help='Print table as CSV [Default: %default]')
parser.add_option('--cuda',
dest='cuda',
default=False,
action='store_true',
help='Predict on the GPU [Default: %default]')
parser.add_option('--cudnn',
dest='cudnn',
default=False,
action='store_true',
help='Predict on the GPU w/ CuDNN [Default: %default]')
parser.add_option(
'-d',
dest='model_hdf5_file',
default=None,
help='Pre-computed model output as HDF5 [Default: %default]')
parser.add_option(
'--dense',
dest='dense_table',
default=False,
action='store_true',
help=
'Print a dense SNP x Targets table, as opposed to a SNP/Target pair per line [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/data/genomes/hg19.fa' % os.environ['BASSETDIR'],
help=
'Genome FASTA from which sequences will be drawn [Default: %default]')
parser.add_option(
'--f1',
dest='genome1_fasta',
default=None,
help='Genome FASTA which which major allele sequences will be drawn')
parser.add_option(
'--f2',
dest='genome2_fasta',
default=None,
help='Genome FASTA which which minor allele sequences will be drawn')
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(
'-l',
dest='seq_len',
type='int',
default=1000,
help='Sequence length provided to the model [Default: %default]')
parser.add_option('-m',
dest='min_limit',
default=0.1,
type='float',
help='Minimum heatmap limit [Default: %default]')
parser.add_option(
'-o',
dest='out_dir',
default='sad',
help='Output directory for tables and plots [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='targets_file',
default=None,
help='File specifying target indexes and labels in table format')
(options, args) = parser.parse_args()
if len(args) != 2:
parser.error('Must provide Torch model and VCF file')
else:
model_th = args[0]
vcf_file = args[1]
if not os.path.isdir(options.out_dir):
os.mkdir(options.out_dir)
#################################################################
# prep SNP sequences
#################################################################
# load SNPs
snps = vcf.vcf_snps(vcf_file, options.index_snp, options.score,
options.genome2_fasta is not None)
# get one hot coded input sequences
if not options.genome1_fasta or not options.genome2_fasta:
seq_vecs, seq_headers, snps = vcf.snps_seq1(snps, options.seq_len,
options.genome_fasta)
else:
seq_vecs, seq_headers, snps = vcf.snps2_seq1(snps, options.seq_len,
options.genome1_fasta,
options.genome2_fasta)
# reshape sequences for torch
seq_vecs = seq_vecs.reshape(
(seq_vecs.shape[0], 4, 1, seq_vecs.shape[1] // 4))
# write to HDF5
h5f = h5py.File('%s/model_in.h5' % options.out_dir, 'w')
h5f.create_dataset('test_in', data=seq_vecs)
h5f.close()
#################################################################
# predict in Torch
#################################################################
if options.model_hdf5_file is None:
if options.cudnn:
cuda_str = '-cudnn'
elif options.cuda:
cuda_str = '-cuda'
else:
cuda_str = ''
options.model_hdf5_file = '%s/model_out.txt' % options.out_dir
cmd = 'basset_predict.lua -rc %s %s %s/model_in.h5 %s' % (
cuda_str, model_th, options.out_dir, options.model_hdf5_file)
print(cmd)
subprocess.call(cmd, shell=True)
# read in predictions
seq_preds = []
for line in open(options.model_hdf5_file):
seq_preds.append(np.array([np.float16(p) for p in line.split()]))
seq_preds = np.array(seq_preds)
#################################################################
# collect and print SADs
#################################################################
if options.targets_file is None:
target_labels = ['t%d' % ti for ti in range(seq_preds.shape[1])]
else:
target_labels = [
line.split()[0] for line in open(options.targets_file)
]
if options.dense_table:
sad_out = open('%s/sad_table.txt' % options.out_dir, 'w')
else:
header_cols = ('rsid', 'index', 'score', 'ref', 'alt', 'target',
'ref_pred', 'alt pred', 'sad')
if options.csv:
sad_out = open('%s/sad_table.csv' % options.out_dir, 'w')
print(','.join(header_cols), file=sad_out)
else:
sad_out = open('%s/sad_table.txt' % options.out_dir, 'w')
print(' '.join(header_cols), file=sad_out)
# hash by index snp
sad_matrices = {}
sad_labels = {}
sad_scores = {}
pi = 0
for snp in snps:
# get reference prediction
ref_preds = seq_preds[pi, :]
pi += 1
for alt_al in snp.alt_alleles:
# get alternate prediction
alt_preds = seq_preds[pi, :]
pi += 1
# normalize by reference
alt_sad = alt_preds - ref_preds
sad_matrices.setdefault(snp.index_snp, []).append(alt_sad)
# label as mutation from reference
alt_label = '%s_%s>%s' % (snp.rsid, vcf.cap_allele(
snp.ref_allele), vcf.cap_allele(alt_al))
sad_labels.setdefault(snp.index_snp, []).append(alt_label)
# save scores
sad_scores.setdefault(snp.index_snp, []).append(snp.score)
# set index SNP
snp_is = '%-13s' % '.'
if options.index_snp:
snp_is = '%-13s' % snp.index_snp
# set score
snp_score = '%5s' % '.'
if options.score:
snp_score = '%5.3f' % snp.score
# print table line(s)
if options.dense_table:
cols = [
snp.rsid, snp_is, snp_score,
vcf.cap_allele(snp.ref_allele),
vcf.cap_allele(alt_al)
]
for ti in range(len(alt_sad)):
cols += ['%.4f' % ref_preds[ti], '%.4f' % alt_sad[ti]]
sep = ' '
if options.csv:
sep = ','
print(sep.join([str(c) for c in cols]), file=sad_out)
else:
for ti in range(len(alt_sad)):
cols = (snp.rsid, snp_is, snp_score,
vcf.cap_allele(snp.ref_allele),
vcf.cap_allele(alt_al), target_labels[ti],
ref_preds[ti], alt_preds[ti], alt_sad[ti])
if options.csv:
print(','.join([str(c) for c in cols]), file=sad_out)
else:
print('%-13s %s %5s %6s %6s %12s %6.4f %6.4f %7.4f' %
cols,
file=sad_out)
sad_out.close()
#################################################################
# plot SAD heatmaps
#################################################################
if options.heatmaps:
for ii in sad_matrices:
# convert fully to numpy arrays
sad_matrix = abs(np.array(sad_matrices[ii]))
print(ii, sad_matrix.shape)
if sad_matrix.shape[0] > 1:
vlim = max(options.min_limit, sad_matrix.max())
score_mat = np.reshape(np.array(sad_scores[ii]), (-1, 1))
# plot heatmap
plt.figure(figsize=(20, 0.5 + 0.5 * sad_matrix.shape[0]))
if options.score:
# lay out scores
cols = 12
ax_score = plt.subplot2grid((1, cols), (0, 0))
ax_sad = plt.subplot2grid((1, cols), (0, 1),
colspan=(cols - 1))
sns.heatmap(score_mat,
xticklabels=False,
yticklabels=False,
vmin=0,
vmax=1,
cmap='Reds',
cbar=False,
ax=ax_score)
else:
ax_sad = plt.gca()
sns.heatmap(sad_matrix,
xticklabels=target_labels,
yticklabels=sad_labels[ii],
vmin=0,
vmax=vlim,
ax=ax_sad)
for tick in ax_sad.get_xticklabels():
tick.set_rotation(-45)
tick.set_horizontalalignment('left')
tick.set_fontsize(5)
plt.tight_layout()
if ii == '.':
out_pdf = '%s/sad_heat.pdf' % options.out_dir
else:
out_pdf = '%s/sad_%s_heat.pdf' % (options.out_dir, ii)
plt.savefig(out_pdf)
plt.close()
