Mercurial > repos > estrain > microrunqc
view run_fastq_scan.py @ 3:9ce4c66690cf draft
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author | estrain |
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date | Fri, 10 Mar 2023 14:39:38 +0000 |
parents | a53acd38d77e |
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#!/usr/bin/env ## Run fastq-scan to get mean read length and mean quality score ## author: errol strain, estrain@gmail.com from argparse import (ArgumentParser, FileType) import sys import glob import subprocess import json def parse_args(): "Parse the input arguments, use '-h' for help." parser = ArgumentParser(description='Run fastq-scan on a pair of gzipped FASTQ files') # Read inputs parser.add_argument('--fastq', type=str, required=True, nargs=2, help='FASTQ files') parser.add_argument('--output', type=str, required=True, nargs=1, help='Output File') parser.add_argument('--type', type=str, required=True, nargs=1, help='File Type (text or gz)') return parser.parse_args() args =parse_args() # FASTA file r1 = args.fastq[0] r2 = args.fastq[1] # Read 1 if str(args.type[0]) == "gz" : cmd1 = ["zcat", r1] else : cmd1 = ["cat", r1] cmd2 = ["fastq-scan"] pcmd1= subprocess.Popen(cmd1,stdout= subprocess.PIPE,shell=False) r1json = json.loads(subprocess.Popen(cmd2, stdin=pcmd1.stdout,stdout=subprocess.PIPE,shell=False).communicate()[0]) r1q = round(r1json["qc_stats"]["qual_mean"],1) r1l = round(r1json["qc_stats"]["read_mean"],1) # Read 2 if str(args.type[0]) == "gz" : cmd1 = ["zcat", r2] else : cmd1 = ["cat", r2] cmd2 = ["fastq-scan"] pcmd1= subprocess.Popen(cmd1,stdout= subprocess.PIPE,shell=False) r2json = json.loads(subprocess.Popen(cmd2, stdin=pcmd1.stdout,stdout=subprocess.PIPE,shell=False).communicate()[0]) r2q = round(r2json["qc_stats"]["qual_mean"],1) r2l = round(r2json["qc_stats"]["read_mean"],1) # Write output to be used by sum_mlst.py output = open(args.output[0],"w") output.write(str(r1l) + "\t" + str(r2l) + "\t" + str(r1q) + "\t" + str(r2q))