Mercurial > repos > kkonganti > centrifuge_process

comparison process_centrifuge_output.py @ 1:48eebe68ec69

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"planemo upload"
author kkonganti
date Wed, 22 Jun 2022 16:56:23 -0400
parents 00fa638e833e
children
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0:00fa638e833e 1:48eebe68ec69
9 9
10 10
11 def main(): 11 def main():
12 # READ IN ARGUMENTS 12 # READ IN ARGUMENTS
13 desc = """ 13 desc = """
14 This script is part of the centriflaken pipeline: It processes centrifuge 14 This script is part of the CPIPES - centriflaken pipeline: It processes centrifuge
15 output and produces either a filtered FASTQ or a text file of FASTQ IDs based 15 output and produces either a filtered FASTQ or a text file of FASTQ IDs based
16 on the supplied taxa/bug 16 on the supplied taxa/bug
17 """ 17 """
18 parser = argparse.ArgumentParser(prog='process_centrifuge_output.py', description=desc) 18 parser = argparse.ArgumentParser(prog='process_centrifuge_output.py', description=desc)
19 parser.add_argument("-v", dest='verbose', action="store_true", help="For more verbose output") 19 parser.add_argument("-v", dest='verbose', action="store_true", help="For more verbose output")