Mercurial > repos > petr-novak > re_utils
comparison fastq_name_affixer.py @ 3:e320ef2d105a draft
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| author | petr-novak |
|---|---|
| date | Thu, 05 Sep 2019 09:04:56 -0400 |
| parents | |
| children |
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| 2:ff658cf87f16 | 3:e320ef2d105a |
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| 1 #!/usr/bin/env python | |
| 2 import sys | |
| 3 | |
| 4 from optparse import OptionParser | |
| 5 | |
| 6 parser = OptionParser() | |
| 7 parser.add_option("-f", "--fastq", dest="fastq", help="fastq file") | |
| 8 parser.add_option("-p", "--prefix", dest="prefix", help="prefix to be added to names") | |
| 9 parser.add_option("-s", "--suffix", dest="suffix", help="suffix to be added",default='') | |
| 10 parser.add_option("-n", "--nspace", dest="nspace", help="number of spaces to ignore",default='0') | |
| 11 options, args = parser.parse_args() | |
| 12 nspace=int(options.nspace) | |
| 13 | |
| 14 f=open(options.fastq,"r") | |
| 15 j=0 | |
| 16 for oneline in f: | |
| 17 if oneline=="": | |
| 18 continue | |
| 19 j+=1 | |
| 20 if j==5: | |
| 21 j=1 | |
| 22 if not oneline: | |
| 23 break | |
| 24 | |
| 25 if (oneline[0]=="@" and j==1) or (oneline[0]=="+" and len(oneline)>2 and j==3): | |
| 26 header=" ".join(oneline.split()[:1+nspace]) | |
| 27 header_out=header[0]+options.prefix+header[1:]+options.suffix+"\n" | |
| 28 sys.stdout.write(header_out) | |
| 29 else: | |
| 30 sys.stdout.write(oneline) | |
| 31 |