Mercurial > repos > estrain > microrunqc

comparison run_fastq_scan.py @ 0:a53acd38d77e draft

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author estrain
date Tue, 24 Mar 2020 08:54:42 -0400
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-1:000000000000 0:a53acd38d77e
1 #!/usr/bin/env
2
3 ## Run fastq-scan to get mean read length and mean quality score
4 ## author: errol strain, estrain@gmail.com
5
6 from argparse import (ArgumentParser, FileType)
7 import sys
8 import glob
9 import subprocess
10 import json
11
12 def parse_args():
13 "Parse the input arguments, use '-h' for help."
14
15 parser = ArgumentParser(description='Run fastq-scan on a pair of gzipped FASTQ files')
16
17 # Read inputs
18 parser.add_argument('--fastq', type=str, required=True, nargs=2, help='FASTQ files')
19 parser.add_argument('--output', type=str, required=True, nargs=1, help='Output File')
20 parser.add_argument('--type', type=str, required=True, nargs=1, help='File Type (text or gz)')
21
22 return parser.parse_args()
23
24 args =parse_args()
25
26 # FASTA file
27 r1 = args.fastq[0]
28 r2 = args.fastq[1]
29
30 # Read 1
31 if str(args.type[0]) == "gz" :
32 cmd1 = ["zcat", r1]
33 else :
34 cmd1 = ["cat", r1]
35 cmd2 = ["fastq-scan"]
36 pcmd1= subprocess.Popen(cmd1,stdout= subprocess.PIPE,shell=False)
37 r1json = json.loads(subprocess.Popen(cmd2, stdin=pcmd1.stdout,stdout=subprocess.PIPE,shell=False).communicate()[0])
38 r1q = round(r1json["qc_stats"]["qual_mean"],1)
39 r1l = round(r1json["qc_stats"]["read_mean"],1)
40
41 # Read 2
42 if str(args.type[0]) == "gz" :
43 cmd1 = ["zcat", r2]
44 else :
45 cmd1 = ["cat", r2]
46 cmd2 = ["fastq-scan"]
47 pcmd1= subprocess.Popen(cmd1,stdout= subprocess.PIPE,shell=False)
48 r2json = json.loads(subprocess.Popen(cmd2, stdin=pcmd1.stdout,stdout=subprocess.PIPE,shell=False).communicate()[0])
49 r2q = round(r2json["qc_stats"]["qual_mean"],1)
50 r2l = round(r2json["qc_stats"]["read_mean"],1)
51
52 # Write output to be used by sum_mlst.py
53 output = open(args.output[0],"w")
54 output.write(str(r1l) + "\t" + str(r2l) + "\t" + str(r1q) + "\t" + str(r2q))