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QC_stats_Final.py
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QC_stats_Final.py
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#!/usr/bin/python
import os
import pysam
import re
import shlex
import string
import subprocess
import tempfile
from numpy import array
from sys import argv
def _count_reads(bam):
stats = { 'total_reads' : 0, 'mapped_reads' : 0 }
with pysam.Samfile(bam, 'rb') as bam_file:
for read in bam_file:
stats['total_reads'] += 1
if (not read.is_unmapped):
stats['mapped_reads'] += 1
stats['percent_mapped'] = (float(stats['mapped_reads']) / float(stats['total_reads'])) * 100
stats['percent_mapped'] = "%2.2F" % stats['percent_mapped'] + '%'
return stats
def _coverage(bam):
samtools = '/usr/local/apps/samtools/1.2/bin/samtools';
intersectbed = '/usr/local/apps/bedtools/2.24.0/bin/intersectBed'
targets = argv[2]
cmd = '%s view -F 0x0400 -b "%s" | %s depth -q 20 -Q 30 -b %s /dev/stdin | awk -v OFS="\\t" \'{print $1,$2-1,$2,$3}\' | %s -a stdin -b %s -wo' % (samtools, bam, samtools, targets, intersectbed, targets)
proc = subprocess.Popen(["-c", cmd], stdin=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)
stats = {}
total_positions = 0
positions_at_1000 = 0
positions_at_400 = 0
positions_at_200 = 0
positions_at_100 = 0
positions_at_50 = 0
positions_at_30 = 0
positions_at_20 = 0
positions_at_15 = 0
positions_at_10 = 0
positions_at_5 = 0
targets_fh = open(targets, 'r')
for line in targets_fh:
line = line.rstrip(os.linesep)
cols = line.split("\t")
start = int(cols[1])
end = int(cols[2])
total_positions += (end - start)
for line in proc.stdout:
line = line.rstrip(os.linesep)
cols = line.split("\t")
chr = cols[0]
pos = cols[2]
depth = int(cols[3])
if (depth >= 1000):
positions_at_1000 += 1
if (depth >= 400):
positions_at_400 += 1
if (depth >= 200):
positions_at_200 += 1
if (depth >= 100):
positions_at_100 += 1
if (depth >= 50):
positions_at_50 += 1
if (depth >= 30):
positions_at_30 += 1
if (depth >= 20):
positions_at_20 +=1
if (depth >= 15):
positions_at_15 +=1
if (depth >= 10):
positions_at_10 +=1
if (depth >= 5):
positions_at_5 +=1
stats['percent_at_1000'] = (float(positions_at_1000) /
float(total_positions)) * 100
stats['percent_at_1000'] = "%2.2F" % stats['percent_at_1000'] + '%'
stats['percent_at_400'] = (float(positions_at_400) /
float(total_positions)) * 100
stats['percent_at_400'] = "%2.2F" % stats['percent_at_400'] + '%'
stats['percent_at_200'] = (float(positions_at_200) /
float(total_positions)) * 100
stats['percent_at_200'] = "%2.2F" % stats['percent_at_200'] + '%'
stats['percent_at_100'] = (float(positions_at_100) /
float(total_positions)) * 100
stats['percent_at_100'] = "%2.2F" % stats['percent_at_100'] + '%'
stats['percent_at_50'] = (float(positions_at_50) /
float(total_positions)) * 100
stats['percent_at_50'] = "%2.2F" % stats['percent_at_50'] + '%'
stats['percent_at_30'] = (float(positions_at_30) /
float(total_positions)) * 100
stats['percent_at_30'] = "%2.2F" % stats['percent_at_30'] + '%'
stats['percent_at_20'] = (float(positions_at_20) /
float(total_positions)) * 100
stats['percent_at_20'] = "%2.2F" % stats['percent_at_20'] + '%'
stats['percent_at_15'] = (float(positions_at_15) /
float(total_positions)) * 100
stats['percent_at_15'] = "%2.2F" % stats['percent_at_15'] + '%'
stats['percent_at_10'] = (float(positions_at_10) /
float(total_positions)) * 100
stats['percent_at_10'] = "%2.2F" % stats['percent_at_10'] + '%'
stats['percent_at_5'] = (float(positions_at_5) /
float(total_positions)) * 100
stats['percent_at_5'] = "%2.2F" % stats['percent_at_5'] + '%'
return stats
def _ontarget(bam):
intersectbed = '/usr/local/apps/bedtools/2.24.0/bin/intersectBed'
targets = argv[2]
ontarget_bam = "%s_ontarget.bam" % (os.path.basename(bam))
## os.getenv('USER', default_value)
temp = tempfile.NamedTemporaryFile(dir='/scratch/tyagim/')
cmd = '%s -abam "%s" -b %s' % (intersectbed, bam, targets)
args = shlex.split(cmd)
subprocess.check_call(args, stdout=temp)
temp.seek(0)
stats = { 'ontarget_reads' : 0, 'unique_ontarget_reads' : 0, 'hq_unique_ontarget_reads': 0 }
min_mapq = 999999999
mapq_array = [ ]
with pysam.Samfile(temp.name, 'rb') as bam_file:
for read in bam_file:
stats['ontarget_reads'] += 1
if (not read.is_duplicate):
stats['unique_ontarget_reads'] += 1
mapq_array.append(read.mapq)
if (read.mapq < min_mapq):
min_mapq = read.mapq
if (read.mapq >= 30):
stats['hq_unique_ontarget_reads'] += 1
numpy_array = array(mapq_array)
stats['min_mapq'] = min_mapq
stats['mean_mapq'] = numpy_array.mean()
stats['stddev_mapq'] = numpy_array.std()
return stats
print string.join(['sample',
'total_reads', 'mapped_reads',
'percent_mapped',
'ontarget_reads', 'percent_ontarget',
'unique_ontarget_reads',
'percent_unique_ontarget',
'min_mapq',
'mean_mapq',
'stddev_mapq',
'hq_unique_ontarget_reads',
'percent_hq_unique_ontarget',
'percent_hq_unique_positions_at_5x',
'percent_hq_unique_positions_at_10x',
'percent_hq_unique_positions_at_15x',
'percent_hq_unique_positions_at_20x',
'percent_hq_unique_positions_at_30x',
'percent_hq_unique_positions_at_50x',
'percent_hq_unique_positions_at_100x',
'percent_hq_unique_positions_at_200x',
'percent_hq_unique_positions_at_400x',
'percent_hq_unique_positions_at_1000x'
], "\t")
for filename in [argv[1]]:
m = re.search('(.+)\.final\.bam$', filename)
if (m is not None):
sample = m.group(1)
stats1 = _count_reads(filename)
stats2 = _ontarget(filename)
stats3 = _coverage(filename)
stats2['percent_ontarget'] = (float(stats2['ontarget_reads']) /
float(stats1['mapped_reads'])) * 100
stats2['percent_ontarget'] = "%2.2F" % stats2['percent_ontarget'] + '%'
stats2['percent_unique_ontarget'] = (float(stats2['unique_ontarget_reads']) /
float(stats2['ontarget_reads'])) * 100
stats2['percent_unique_ontarget'] = "%2.2F" % stats2['percent_unique_ontarget'] + '%'
stats2['percent_hq_unique_ontarget'] = (float(stats2['hq_unique_ontarget_reads']) /
float(stats2['unique_ontarget_reads'])) * 100
stats2['percent_hq_unique_ontarget'] = "%2.2F" % stats2['percent_hq_unique_ontarget'] + '%'
print string.join([sample,
str(stats1['total_reads']),
str(stats1['mapped_reads']),
str(stats1['percent_mapped']),
str(stats2['ontarget_reads']),
str(stats2['percent_ontarget']),
str(stats2['unique_ontarget_reads']),
str(stats2['percent_unique_ontarget']),
str(stats2['min_mapq']),
str(stats2['mean_mapq']),
str(stats2['stddev_mapq']),
str(stats2['hq_unique_ontarget_reads']),
str(stats2['percent_hq_unique_ontarget']),
str(stats3['percent_at_5']),
str(stats3['percent_at_10']),
str(stats3['percent_at_15']),
str(stats3['percent_at_20']),
str(stats3['percent_at_30']),
str(stats3['percent_at_50']),
str(stats3['percent_at_100']),
str(stats3['percent_at_200']),
str(stats3['percent_at_400']),
str(stats3['percent_at_1000']),
], "\t"), "\n";