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fastq_metrics.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
from subprocess import call
import os
from threading import Thread
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("-i", "--input", help="FASTQ file (can be the location on S3)", nargs='+')
parser.add_argument("-n", "--cores", help="Number of Cores to use")
args = parser.parse_args()
fastq_files = args.input
n_cores = int(args.cores)
print(fastq_files)
print(len(fastq_files))
#mock up
# fastq_file = "../../../input/bam/test.recal.bam"
input_folder = "/home/ubuntu/projects/input/fastq"
#download all fastq files
list_fastq_file = []
for fastq_file in fastq_files:
base=os.path.basename(fastq_file)
print(base)
if fastq_file.startswith('s3://'):
#download file to input folder
command = "s3cmd get --continue %s %s/" % (fastq_file, input_folder)
output = call(command, shell=True)
print(output)
fastq_file = "%s/%s" % (input_folder, base)
list_fastq_file.append(fastq_file)
# base_name = os.path.splitext(base)[0]
base_name = base.split('.')[0]
print(base_name)
memory_use = "16g"
#create one folder per sample
output_folder = "/home/ubuntu/projects/output/reports/fastq/"
if not os.path.exists(output_folder):
os.makedirs(output_folder)
fastqc_dir = "/home/ubuntu/projects/programs/fastqc/FastQC/"
qualimap_dir = "/home/ubuntu/projects/programs/qualimap/qualimap_v2.2"
#s3
#if bam file start with s3 download from s3
#fastqc
command = "%s/fastqc -t %s %s -o %s" % (fastqc_dir, n_cores, " ".join(list_fastq_file), output_folder)
output = call(command, shell=True)
print(output)
#done already!
#removefastq
# os.remove(fastq_file)
# print('Running featureCounts')
# #featureCounts
# command = """/home/ubuntu/projects/programs/subread-1.5.1-Linux-x86_64/bin/featureCounts --donotsort -T 4 -p \
# -a /home/ubuntu/projects/input/gtf/Homo_sapiens.GRCh37.75.gtf \
# -o %s/%s.featureCounts.txt \
# %s""" % (output_folder, base_name, fastq_file)
# #bamtools
# print('Running bamtools')
# command = """/home/ubuntu/projects/programs/bamtools/bin/bamtools stats -in %s > %s/%s.bamtools.stats.txt""" % (fastq_file, output_folder, base_name)
# # output = call(command, shell=True)
# # print(output)
# print('Running DepthOfCoverage')
# #gatk DepthOfCoverage
# command = """
# java -Xmx15g -jar %s/GenomeAnalysisTK.jar -T DepthOfCoverage \
# -I %s \
# -R %s \
# -o %s/%s.DepthOfCoverage.txt \
# -nt 4 \
# --omitIntervalStatistics \
# -ct 5 -ct 10 -ct 20 -ct 30 \
# -log %s/%s.DepthofCoverage.log \
# """ % (gatk_dir, fastq_file, human_reference, output_folder, base_name, output_folder, base_name)
# output = call(command, shell=True)
# print(output)
# #qualimap BamQC
# print('Running qualimap BamQC')
# command = """%s/qualimap bamqc \
# --java-mem-size=15G \
# -bam %s \
# -outdir %s \
# -nt 4
# """ % (qualimap_dir, fastq_file, output_folder)
# # 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, fastq_file, output_folder, base_name)
# # output = call(command, shell=True)
# # print(output)
# # #picard
# # print('Running CollectAlignmentSummaryMetrics')
# # # #CollectAlignmentSummaryMetrics
# # command = """
# # java -jar -Xmx15g %s/picard.jar CollectAlignmentSummaryMetrics \
# # I=%s \
# # O=%s/%s.AlignmentSummaryMetrics.txt \
# # R=%s \
# # VALIDATION_STRINGENCY=SILENT""" % (picard_dir, fastq_file, output_folder, base_name, human_reference)
# # output = call(command, shell=True)
# # print(output)
# # print('Running CollectGcBiasMetrics')
# # # #CollectGcBiasMetrics
# # command = """
# # java -jar -Xmx15g %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""" % (picard_dir, fastq_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%s -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_use, picard_dir, fastq_file, output_folder, base_name, output_folder, base_name)
# # output = call(command, shell=True)
# # print(output)
# # # #MeanQualityByCycle
# # print('Running MeanQualityByCycle')
# # command = """java -Xmx%s -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_use, picard_dir, fastq_file, output_folder, base_name, output_folder, base_name)
# # output = call(command, shell=True)
# # print(output)
# # print('Running QualityScoreDistribution')
# # # #QualityScoreDistribution
# # command = """java -Xmx%s -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_use, picard_dir, fastq_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, fastq_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 \
# # BAIT_INTERVALS=%s \
# # TARGET_INTERVALS=%s \
# # VALIDATION_STRINGENCY=SILENT """ % (memory_use, picard_dir, fastq_file, output_folder, base_name, human_reference, target_file, target_file)
# # output = call(command, shell=True)
# # print(output)