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one_bam_genome_metrics.py
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one_bam_genome_metrics.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
from subprocess import call, check_output#, run
import subprocess
import os
from multiprocessing import Pool
import time
import argparse
import logging
def chunks(l, n):
"""Yield successive n-sized chunks from l."""
for i in range(0, len(l), n):
yield l[i:i + n]
parser = argparse.ArgumentParser()
parser.add_argument("-i", "--input", help="BAM file (can be the location on S3)")
parser.add_argument("-n", "--cores", help="Number of Cores to use")
parser.add_argument("-m", "--memory", help="RAM Memory to use in GB")
args = parser.parse_args()
bam_file = args.input
print(bam_file)
# original_bam = bam_file
n_cores = int(args.cores)
memory = int(args.memory)
# print(bam_file)
human_reference = "/home/ubuntu/projects/input/b37/human_g1k_v37.fasta" #84 features
human_reference = "/home/ubuntu/projects/input/grch37/d5/hs37d5.fa" #86 features
gtf_file = "/home/ubuntu/projects/input/gtf/Homo_sapiens.GRCh37.75.gtf"
fastqc_dir = "/home/ubuntu/projects/programs/fastqc/FastQC/"
samtools_dir = "/home/ubuntu/projects/programs/samtools-1.3.1"
bamtools_dir = "/home/ubuntu/projects/programs/bamtools/bin/bamtools"
programs_dir = "/home/ubuntu/projects/programs/"
picard_dir = "/home/ubuntu/projects/programs/picard"
gatk_dir = "/home/ubuntu/projects/programs/gatk"
qualimap_dir = "/home/ubuntu/projects/programs/qualimap/qualimap_v2.2"
featurecounts_dir = "/home/ubuntu/projects/programs/subread-1.5.1-Linux-x86_64/bin"
input_folder = '/home/ubuntu/projects/input/bam'
base=os.path.basename(bam_file)
base_name = os.path.splitext(base)[0]
# print(base, base_name)
output_folder = '/home/ubuntu/projects/output/bam/%s' % (base_name)
if not os.path.exists(output_folder):
os.makedirs(output_folder)
logging.basicConfig(filename='%s.run.log.txt' % (base_name),level=logging.DEBUG)
# print(base_name)
# print(bam_file)
if bam_file.startswith('s3://'):
#download file to input folder
command = "s3cmd get --continue %s %s/" % (bam_file, input_folder)
output = call(command, shell=True)
logging.info(output)
print(output)
# print(command)
bam_file = "%s/%s" % (input_folder, base)
print(bam_file)
if not os.path.exists(bam_file+'.bai'):
#Download index
command = "s3cmd get --continue %s.bai %s/" % (original_bam, input_folder)
output = call(command, shell=True)
logging.info(output)
print(output)
command = "%s/fastqc -t %s %s -o %s &" % (fastqc_dir, n_cores, bam_file, output_folder)
# print(command)
# output = call(command, shell=True)
# print(output)
# #samtools flagstat
# print('Running samtools flagstat')
# command = """%s/samtools flagstat %s > %s/%s.samtools.flagstat.txt
# """ % (samtools_dir, bam_file, output_folder, base_name)
# output = call(command, shell=True)
# print(output)
#samtools flagstat
print('Running sambamba flagstat')
command = """%s/sambamba_v0.6.4 flagstat -t %s -p %s > %s/%s.samtools.flagstat.txt &
""" % (programs_dir, n_cores, bam_file, output_folder, base_name)
# output = call(command, shell=True)
# print(output)
print('Running featureCounts')
#featureCounts
command = """%s/featureCounts --donotsort -T %s -p \
-a %s \
-o %s/%s.featureCounts.txt \
%s &""" % (featurecounts_dir, n_cores, gtf_file, output_folder, base_name, bam_file)
# output = call(command, shell=True)
# print(output)
print('Running DepthOfCoverage')
#gatk DepthOfCoverage
command = """
java -Xmx%sg -jar %s/GenomeAnalysisTK.jar -T DepthOfCoverage \
-I %s \
-R %s \
-o %s/%s.DepthOfCoverage.txt \
-ct 15 -ct 50 -ct 100 -ct 150 -ct 200 \
-log %s/%s.DepthofCoverage.log \
--omitIntervalStatistics \
-nt %s &
""" % (memory, gatk_dir, bam_file, human_reference, output_folder, base_name, output_folder, base_name, n_cores)
output = call(command, shell=True)
print(output)
#qualimap BamQC
print('Running qualimap BamQC')
command = """%s/qualimap bamqc \
--java-mem-size=%sG \
-bam %s \
-outdir %s \
-nt %s &
""" % (qualimap_dir, memory, bam_file, output_folder, n_cores)
# output = call(command, shell=True)
# print(output)
# os.remove(bam_file)
#bamtools do not run in parallel
# print('Running bamtools')
# command = """/home/ubuntu/projects/programs/bamtools/bin/bamtools stats -in %s > %s/%s.bamtools.stats.txt""" % (bam_file, output_folder, base_name)
# output = call(command, shell=True)
# print(output)
# #picard
# print('Running CollectAlignmentSummaryMetrics')
# # #CollectAlignmentSummaryMetrics
# command = """
# java -jar -Xmx%sg %s/picard.jar CollectAlignmentSummaryMetrics \
# I=%s \
# O=%s/%s.AlignmentSummaryMetrics.txt \
# R=%s \
# VALIDATION_STRINGENCY=SILENT""" % (memory, picard_dir, bam_file, output_folder, base_name, human_reference)
# output = call(command, shell=True)
# print(output)
# print('Running CollectGcBiasMetrics')
# # #CollectGcBiasMetrics
# command = """
# java -jar -Xmx%sg %s/picard.jar CollectGcBiasMetrics \
# I=%s \
# O=%s/%s.gc_bias_metrics.txt \
# R=%s \
# CHART=%s/%s.gc_bias_metrics.pdf \
# S=%s/%s.gc_bias_summary_metrics.txt \
# VALIDATION_STRINGENCY=SILENT""" % (memory, picard_dir, bam_file, output_folder, base_name, human_reference, output_folder, base_name, output_folder, base_name)
# output = call(command, shell=True)
# print(output)
# print('Running CollectInsertSizeMetrics')
# #CollectInsertSizeMetrics
# command = """java -Xmx%sg -jar %s/picard.jar CollectInsertSizeMetrics \
# I=%s \
# O=%s/%s.insert_size_metrics.txt \
# H=%s/%s.insert_size_histogram.pdf \
# M=0.5 \
# VALIDATION_STRINGENCY=SILENT""" % (memory, picard_dir, bam_file, output_folder, base_name, output_folder, base_name)
# output = call(command, shell=True)
# print(output)
# # #MeanQualityByCycle
# print('Running MeanQualityByCycle')
# command = """java -Xmx%sg -jar %s/picard.jar MeanQualityByCycle \
# I=%s \
# O=%s/%s.mean_qual_by_cycle.txt \
# CHART=%s/%s.mean_qual_by_cycle.pdf \
# VALIDATION_STRINGENCY=SILENT """ % (memory, picard_dir, bam_file, output_folder, base_name, output_folder, base_name)
# output = call(command, shell=True)
# print(output)
# print('Running QualityScoreDistribution')
# # #QualityScoreDistribution
# command = """java -Xmx%sg -jar %s/picard.jar QualityScoreDistribution \
# I=%s \
# O=%s/%s.qual_score_dist.txt \
# CHART=%s/%s.qual_score_dist.pdf \
# VALIDATION_STRINGENCY=SILENT """ % (memory, picard_dir, bam_file, output_folder, base_name, output_folder, base_name)
# output = call(command, shell=True)
# print(output)
# print('Running BamIndexStats')
# # #BamIndexStats
# command = """java -Xmx%s -jar %s/picard.jar BamIndexStats \
# I=%s \
# O=%s/%s.BamIndexStats.output.txt \
# VALIDATION_STRINGENCY=SILENT""" % (memory_use, picard_dir, bam_file, output_folder, base_name)
# output = call(command, shell=True)
# print(output)
# print('Running CollectHsMetrics')
#CollectHsMetrics
# command = """java -Xmx%s -jar %s/picard.jar CollectHsMetrics \
# I=%s \
# O=%s/%s.hs_metrics.txt \
# R=%s \
# VALIDATION_STRINGENCY=SILENT """ % (memory_use, picard_dir, bam_file, output_folder, base_name, human_reference)
# output = call(command, shell=True)
# print(output)