Mercurial > repos > jowong > add_sample_as_first_line
view add_sample_name_as_first_line.py @ 3:98f9da980bf5 draft default tip
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit f3fe76f6cbf17b0ec4162065206483652a6519b7-dirty
author | jowong |
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date | Fri, 09 Nov 2018 12:27:57 -0500 |
parents | 74a9f37e2bc9 |
children |
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import sys import argparse import re def Parser(): the_parser = argparse.ArgumentParser(description="add label to first line of file") the_parser.add_argument('--input', required=True, action="store", type=str, help="input file") the_parser.add_argument('--output', required=True, action="store", type=str, help="output file path") the_parser.add_argument('--sample', required=True, action="store", type=str, help="label to add in the first line") args = the_parser.parse_args() return args args=Parser() #input=open(args.input) #output=open(args.output, 'w') #print >> output, args.label #print >> output, input sample_name = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', args.sample.rstrip().lstrip()) with open(args.input) as input: with open(args.output, 'w') as output: output.write(sample_name+"\n") for line in input: output.write(line) #input.close() #output.close()