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