def plot_weblogo(ax, seq, sat_loss_ti, min_limit):
""" Plot height-weighted weblogo sequence.
Args:
ax (Axis): matplotlib axis to plot to.
seq ([ACGT]): DNA sequence
sat_loss_ti (L_sm array): Minimum mutation delta across satmut length.
min_limit (float): Minimum heatmap limit.
"""
# trim sequence to the satmut region
satmut_len = len(sat_loss_ti)
satmut_start = int((len(seq) - satmut_len) // 2)
satmut_seq = seq[satmut_start:satmut_start + satmut_len]
# determine nt heights
vlim = max(min_limit, np.max(-sat_loss_ti))
seq_heights = 0.1 + 1.9 / vlim * (-sat_loss_ti)
# make logo as eps
eps_fd, eps_file = tempfile.mkstemp()
seq_logo(satmut_seq, seq_heights, eps_file, color_mode='meme')
# convert to png
png_fd, png_file = tempfile.mkstemp()
subprocess.call(
'convert -density 1200 %s %s' % (eps_file, png_file), shell=True)
# plot
logo = Image.open(png_file)
ax.imshow(logo)
ax.set_axis_off()
# clean up
os.close(eps_fd)
os.remove(eps_file)
os.close(png_fd)
os.remove(png_file)
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_file> <input_file>'
parser = OptionParser(usage)
parser.add_option('-a', dest='input_activity_file', help='Optional activity table corresponding to an input FASTA file')
parser.add_option('-d', dest='model_hdf5_file', default=None, help='Pre-computed model output as HDF5 [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('-m', dest='min_limit', default=0.1, type='float', help='Minimum heatmap limit [Default: %default]')
parser.add_option('-n', dest='center_nt', default=0, type='int', help='Center nt to mutate and plot in the heat map [Default: %default]')
parser.add_option('-o', dest='out_dir', default='heat', help='Output directory [Default: %default]')
parser.add_option('-p', dest='print_table_all', default=False, action='store_true', help='Print all targets to the table [Default: %default]')
parser.add_option('-r', dest='rng_seed', default=1, type='float', help='Random number generator seed [Default: %default]')
parser.add_option('-s', dest='sample', default=None, type='int', help='Sample sequences from the test set [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 sequences (as a FASTA file or test data in an HDF file')
else:
model_file = args[0]
input_file = args[1]
if not os.path.isdir(options.out_dir):
os.mkdir(options.out_dir)
random.seed(options.rng_seed)
#################################################################
# parse input file
#################################################################
try:
# input_file is FASTA
# load sequences and headers
seqs = []
seq_headers = []
for line in open(input_file):
if line[0] == '>':
seq_headers.append(line[1:].rstrip())
seqs.append('')
else:
seqs[-1] += line.rstrip()
model_input_hdf5 = '%s/model_in.h5'%options.out_dir
if options.input_activity_file:
# one hot code
seqs_1hot, targets = dna_io.load_data_1hot(input_file, options.input_activity_file, mean_norm=False, whiten=False, permute=False, sort=False)
# read in target names
target_labels = open(options.input_activity_file).readline().strip().split('\t')
else:
# load sequences
seqs_1hot = dna_io.load_sequences(input_file, permute=False)
targets = None
target_labels = None
# sample
if options.sample:
sample_i = np.array(random.sample(xrange(seqs_1hot.shape[0]), options.sample))
seqs_1hot = seqs_1hot[sample_i]
seq_headers = seq_headers[sample_i]
if targets is not None:
targets = targets[sample_i]
# reshape sequences for torch
seqs_1hot = seqs_1hot.reshape((seqs_1hot.shape[0],4,1,seqs_1hot.shape[1]/4))
# write as test data to a HDF5 file
h5f = h5py.File(model_input_hdf5, 'w')
h5f.create_dataset('test_in', data=seqs_1hot)
h5f.close()
except (IOError, IndexError):
# input_file is HDF5
try:
model_input_hdf5 = input_file
# load (sampled) test data from HDF5
hdf5_in = h5py.File(input_file, 'r')
seqs_1hot = np.array(hdf5_in['test_in'])
targets = np.array(hdf5_in['test_out'])
try: # TEMP
seq_headers = np.array(hdf5_in['test_headers'])
target_labels = np.array(hdf5_in['target_labels'])
except:
seq_headers = None
target_labels = None
hdf5_in.close()
# sample
if options.sample:
sample_i = np.array(random.sample(xrange(seqs_1hot.shape[0]), options.sample))
seqs_1hot = seqs_1hot[sample_i]
seq_headers = seq_headers[sample_i]
targets = targets[sample_i]
# write sampled data to a new HDF5 file
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()
# convert to ACGT sequences
seqs = dna_io.vecs2dna(seqs_1hot)
except IOError:
parser.error('Could not parse input file as FASTA or HDF5.')
#################################################################
# 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)
print torch_cmd
subprocess.call(torch_cmd, shell=True)
#################################################################
# 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
seq_len = len(seqs[0])
delta_start = 0
delta_len = seq_mod_preds.shape[2]
if delta_len < seq_len:
delta_start = (seq_len - delta_len)/2
for i in range(len(seqs)):
seqs[i] = seqs[i][delta_start:delta_start+delta_len]
# decide which cells to plot
if options.targets == '-1':
plot_targets = xrange(seq_mod_preds.shape[3])
else:
plot_targets = [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]):
try:
header = seq_headers[si]
except TypeError:
header = 'seq%d' % si
seq = seqs[si]
# plot some descriptive heatmaps for each individual cell type
for ci in plot_targets:
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_filename(header), ci)
seq_logo(seq, seq_heights, logo_eps)
# add to figure
logo_png = '%s.png' % logo_eps[:-4]
subprocess.call('convert -density 300 %s %s' % (logo_eps, logo_png), shell=True)
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
#################################################################
print_targets = plot_targets
if options.print_table_all:
print_targets = range(seq_mod_preds.shape[3])
for ci in print_targets:
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_file> <input_file>'
parser = OptionParser(usage)
parser.add_option(
'-a',
dest='input_activity_file',
help='Optional activity table corresponding to an input FASTA file')
parser.add_option(
'-d',
dest='model_hdf5_file',
default=None,
help='Pre-computed model output as HDF5 [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('-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='Center nt to mutate and plot in the heat map [Default: %default]'
)
parser.add_option('-o',
dest='out_dir',
default='heat',
help='Output directory [Default: %default]')
parser.add_option(
'-s',
dest='sample',
default=None,
type='int',
help='Sample sequences from the test set [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 sequences (as a FASTA file or test data in an HDF file'
)
else:
model_file = args[0]
input_file = args[1]
if not os.path.isdir(options.out_dir):
os.mkdir(options.out_dir)
#################################################################
# parse input file
#################################################################
try:
# input_file is FASTA
# load sequences and headers
seqs = []
seq_headers = []
for line in open(input_file):
if line[0] == '>':
seq_headers.append(line[1:].rstrip())
seqs.append('')
else:
seqs[-1] += line.rstrip()
model_input_hdf5 = '%s/model_in.h5' % options.out_dir
if options.input_activity_file:
# one hot code
seqs_1hot, targets = dna_io.load_data_1hot(
input_file,
options.input_activity_file,
mean_norm=False,
whiten=False,
permute=False,
sort=False)
# read in target names
target_labels = open(
options.input_activity_file).readline().strip().split('\t')
else:
# load sequences
seqs_1hot = dna_io.load_sequences(input_file, permute=False)
targets = None
target_labels = None
# sample
if options.sample:
sample_i = np.array(
random.sample(xrange(seqs_1hot.shape[0]), options.sample))
seqs_1hot = seqs_1hot[sample_i]
seq_headers = seq_headers[sample_i]
if targets is not None:
targets = targets[sample_i]
# reshape sequences for torch
seqs_1hot = seqs_1hot.reshape(
(seqs_1hot.shape[0], 4, 1, seqs_1hot.shape[1] / 4))
# write as test data to a HDF5 file
h5f = h5py.File(model_input_hdf5, 'w')
h5f.create_dataset('test_in', data=seqs_1hot)
h5f.close()
except (IOError, IndexError):
# input_file is HDF5
try:
model_input_hdf5 = input_file
# load (sampled) test data from HDF5
hdf5_in = h5py.File(input_file, 'r')
seqs_1hot = np.array(hdf5_in['test_in'])
targets = np.array(hdf5_in['test_out'])
try: # TEMP
seq_headers = np.array(hdf5_in['test_headers'])
target_labels = np.array(hdf5_in['target_labels'])
except:
seq_headers = None
target_labels = None
hdf5_in.close()
# sample
if options.sample:
sample_i = np.array(
random.sample(xrange(seqs_1hot.shape[0]), options.sample))
seqs_1hot = seqs_1hot[sample_i]
seq_headers = seq_headers[sample_i]
targets = targets[sample_i]
# write sampled data to a new HDF5 file
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()
# convert to ACGT sequences
seqs = dna_io.vecs2dna(seqs_1hot)
except IOError:
parser.error('Could not parse input file as FASTA or HDF5.')
#################################################################
# 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)
print torch_cmd
subprocess.call(torch_cmd, shell=True)
#################################################################
# 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
seq_len = len(seqs[0])
delta_start = 0
delta_len = seq_mod_preds.shape[2]
if delta_len < seq_len:
delta_start = (seq_len - delta_len) / 2
for i in range(len(seqs)):
seqs[i] = seqs[i][delta_start:delta_start + delta_len]
# decide which cells to plot
if options.targets == '-1':
plot_targets = xrange(seq_mod_preds.shape[3])
else:
plot_targets = [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]):
try:
header = seq_headers[si]
except TypeError:
header = 'seq%d' % si
seq = seqs[si]
# plot some descriptive heatmaps for each individual cell type
for ci in plot_targets:
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_filename(header), ci)
seq_logo(seq, seq_heights, logo_eps)
# add to figure
logo_png = '%s.png' % logo_eps[:-4]
subprocess.call('convert -density 300 %s %s' %
(logo_eps, logo_png),
shell=True)
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_file> <input_file>"
parser = OptionParser(usage)
parser.add_option(
"-a", dest="input_activity_file", help="Optional activity table corresponding to an input FASTA file"
)
parser.add_option(
"-d", dest="model_hdf5_file", default=None, help="Pre-computed model output as HDF5 [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(
"-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="Center nt to mutate and plot in the heat map [Default: %default]",
)
parser.add_option("-o", dest="out_dir", default="heat", help="Output directory [Default: %default]")
parser.add_option(
"-s", dest="sample", default=None, type="int", help="Sample sequences from the test set [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 sequences (as a FASTA file or test data in an HDF file")
else:
model_file = args[0]
input_file = args[1]
if not os.path.isdir(options.out_dir):
os.mkdir(options.out_dir)
#################################################################
# parse input file
#################################################################
try:
# input_file is FASTA
# load sequences and headers
seqs = []
seq_headers = []
for line in open(input_file):
if line[0] == ">":
seq_headers.append(line[1:].rstrip())
seqs.append("")
else:
seqs[-1] += line.rstrip()
model_input_hdf5 = "%s/model_in.h5" % options.out_dir
if options.input_activity_file:
# one hot code
seqs_1hot, targets = dna_io.load_data_1hot(
input_file, options.input_activity_file, mean_norm=False, whiten=False, permute=False, sort=False
)
# read in target names
target_labels = open(options.input_activity_file).readline().strip().split("\t")
else:
# load sequences
seqs_1hot = dna_io.load_sequences(input_file, permute=False)
targets = None
target_labels = None
# sample
if options.sample:
sample_i = np.array(random.sample(xrange(seqs_1hot.shape[0]), options.sample))
seqs_1hot = seqs_1hot[sample_i]
seq_headers = seq_headers[sample_i]
if targets is not None:
targets = targets[sample_i]
# reshape sequences for torch
seqs_1hot = seqs_1hot.reshape((seqs_1hot.shape[0], 4, 1, seqs_1hot.shape[1] / 4))
# write as test data to a HDF5 file
h5f = h5py.File(model_input_hdf5, "w")
h5f.create_dataset("test_in", data=seqs_1hot)
h5f.close()
except (IOError, IndexError):
# input_file is HDF5
try:
model_input_hdf5 = input_file
# load (sampled) test data from HDF5
hdf5_in = h5py.File(input_file, "r")
seqs_1hot = np.array(hdf5_in["test_in"])
targets = np.array(hdf5_in["test_out"])
try: # TEMP
seq_headers = np.array(hdf5_in["test_headers"])
target_labels = np.array(hdf5_in["target_labels"])
except:
seq_headers = None
target_labels = None
hdf5_in.close()
# sample
if options.sample:
sample_i = np.array(random.sample(xrange(seqs_1hot.shape[0]), options.sample))
seqs_1hot = seqs_1hot[sample_i]
seq_headers = seq_headers[sample_i]
targets = targets[sample_i]
# write sampled data to a new HDF5 file
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()
# convert to ACGT sequences
seqs = dna_io.vecs2dna(seqs_1hot)
except IOError:
parser.error("Could not parse input file as FASTA or HDF5.")
#################################################################
# 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
seq_len = len(seqs[0])
delta_start = 0
delta_len = seq_mod_preds.shape[2]
if delta_len < seq_len:
delta_start = (seq_len - delta_len) / 2
for i in range(len(seqs)):
seqs[i] = seqs[i][delta_start : delta_start + delta_len]
# decide which cells to plot
if options.targets == "-1":
plot_targets = xrange(seq_mod_preds.shape[3])
else:
plot_targets = [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]):
try:
header = seq_headers[si]
except TypeError:
header = "seq%d" % si
seq = seqs[si]
# plot some descriptive heatmaps for each individual cell type
for ci in plot_targets:
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_filename(header), 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()