def get_region_size_metrics(peak_file, out_dir='.'):
'''
From the peak file, return a plot of the region size distribution and
the quartile metrics (summary from R)
'''
import pandas as pd
import numpy as np
import matplotlib as mpl
mpl.use('Agg')
from matplotlib import pyplot as plt
from collections import OrderedDict
basename = os.path.basename(strip_ext_peak(peak_file))
prefix = os.path.join(out_dir, basename)
log = '{}.peak_region_size.qc'.format(prefix)
plot = '{}.peak_region_size.png'.format(prefix)
# Load peak file. If it fails, return nothing as above
peak_df = pd.read_table(peak_file, compression='gzip', header=None)
# Subtract third column from second to get summary
region_sizes = peak_df.iloc[:, 2] - peak_df.iloc[:, 1]
# Summarize and store in ordered dict
peak_summary_stats = region_sizes.describe()
peak_size_summ = OrderedDict([
('Min size', peak_summary_stats['min']),
('25 percentile', peak_summary_stats['25%']),
('50 percentile (median)', peak_summary_stats['50%']),
('75 percentile', peak_summary_stats['75%']),
('Max size', peak_summary_stats['max']),
('Mean', peak_summary_stats['mean']),
])
# Plot density diagram using matplotlib
fig = plt.figure()
ax = fig.add_subplot(111)
y, binEdges = np.histogram(region_sizes, bins=100)
bincenters = 0.5 * (binEdges[1:] + binEdges[:-1])
# write to log file
with open(log, 'w') as fp:
for key, val in peak_size_summ.items():
fp.write(key + '\t' + str(val) + '\n')
plt.plot(bincenters, y, '-')
filename = os.path.basename(peak_file)
ax.set_title('Peak width distribution for {0}'.format(filename))
# write to plot file
fig.savefig(plot, format='png')
return log, plot
def get_num_peaks(peak_file, out_dir='.'):
'''
From the peak file, return number of lines in it
'''
basename = os.path.basename(strip_ext_peak(peak_file))
prefix = os.path.join(out_dir, basename)
log = '{}.num_peak.qc'.format(prefix)
with open(log, 'w') as fp:
fp.write(str(get_num_lines(peak_file)) + '\n')
return log
def peak_to_hammock(peak, out_dir):
peak_type = get_peak_type(peak)
prefix = os.path.join(out_dir, os.path.basename(strip_ext_peak(peak)))
hammock = '{}.{}.hammock'.format(prefix, peak_type)
hammock_tmp = '{}.tmp'.format(hammock)
hammock_tmp2 = '{}.tmp2'.format(hammock)
hammock_gz = '{}.gz'.format(hammock)
hammock_gz_tbi = '{}.gz.tbi'.format(hammock)
if get_num_lines(peak) == 0:
cmd = 'zcat -f {} | gzip -nc > {}'.format(peak, hammock_gz)
run_shell_cmd(cmd)
cmd2 = 'touch {}'.format(hammock_gz_tbi)
else:
cmd = "zcat -f {} | "
cmd += "LC_COLLATE=C sort -k1,1V -k2,2n > {}"
cmd = cmd.format(peak, hammock_tmp)
run_shell_cmd(cmd)
with open(hammock_tmp, 'r') as fin, open(hammock_tmp2, 'w') as fout:
id = 1
for line in fin:
lst = line.rstrip().split('\t')
if peak_type == 'narrowPeak' or peak_type == 'regionPeak':
fout.write(
'{0[0]}\t{0[1]}\t{0[2]}\tscorelst:[{0[6]},{0[7]},'
'{0[8]}],id:{1},'.format(lst, id))
if len(lst[3]) > 1:
fout.write('name:"' + lst[3] + '",')
if lst[5] != '.':
fout.write('strand:"' + lst[5] + '",')
if lst[9] != '-1':
fout.write('sbstroke:[' + lst[9] + ']')
elif peak_type == 'gappedPeak':
fout.write(
'{0[0]}\t{0[1]}\t{0[2]}\tscorelst:[{0[12]},{0[13]},'
'{0[14]}],id:{1},struct:{{thin:[[{0[1]},{0[2]}]],'
'thick:['.format(lst, id))
a = int(lst[1])
sizes = lst[10].split(',')
starts = lst[11].split(',')
for i in range(len(sizes)):
fout.write('[{0},{1}],'.format(
a + int(starts[i]),
a + int(starts[i]) + int(sizes[i])))
fout.write(']},')
if len(lst[3]) > 1:
fout.write('name:"' + lst[3] + '",')
if lst[5] != '.':
fout.write('strand:"' + lst[5] + '",')
elif peak_type == 'broadPeak':
fout.write(
'{0[0]}\t{0[1]}\t{0[2]}\tscorelst:[{0[6]},{0[7]}],'
'id:{1},'.format(lst, id))
if len(lst[3]) > 1:
fout.write('name:"' + lst[3] + '",')
if lst[5] != '.':
fout.write('strand:"' + lst[5] + '",')
else:
raise Exception("Unsupported peak_type {}".format(peak))
id += 1
fout.write('\n')
cmd2 = 'zcat -f {} | sort -k1,1 -k2,2n | bgzip -cf > {}'
cmd2 = cmd2.format(hammock_tmp2, hammock_gz)
run_shell_cmd(cmd2)
cmd3 = 'tabix -f -p bed {}'.format(hammock_gz)
run_shell_cmd(cmd3)
rm_f([hammock, hammock_tmp, hammock_tmp2])
return (hammock_gz, hammock_gz_tbi)
