Mercurial > repos > jowong > add_sample_as_first_line
diff add_sample_name_as_first_line.py @ 0:231b21337c43 draft
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
author | jowong |
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date | Thu, 27 Sep 2018 17:05:18 -0400 |
parents | |
children | 492848eff35d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/add_sample_name_as_first_line.py Thu Sep 27 17:05:18 2018 -0400 @@ -0,0 +1,23 @@ +import sys +import argparse +import re + +def Parser(): + the_parser = argparse.ArgumentParser(description="add sample name as first line of a tab file") + the_parser.add_argument('--input', required=True, action="store", type=str, help="input tab file") + the_parser.add_argument('--output', required=True, action="store", type=str, help="output file") + the_parser.add_argument('--sample', required=True, action="store", type=str, help="sample name to add as the first line of input file") + args = the_parser.parse_args() + return args + +args=Parser() + +sample_name = re.sub('[_12]*.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) + +