Mercurial > repos > mvdbeek > size_distribution

comparison size_distributions.py @ 3:21b5a9170b90 draft

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planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit c8e0a703fcdff580ba0a0c5806a37c088c03ab7b
author mvdbeek
date Mon, 20 Aug 2018 14:27:49 -0400
parents ac5584567084
children f1eeaf42144b
comparison
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2:c8c7b6113241 3:21b5a9170b90
38 df.columns = ['readlength', 'orientation', 'reference', 'count'] 38 df.columns = ['readlength', 'orientation', 'reference', 'count']
39 return df 39 return df
40 40
41 41
42 def write_table(df, output_path): 42 def write_table(df, output_path):
43 df.to_csv(output_path, sep="\t") 43 df.to_csv(output_path, sep="\t", index=False)
44 44
45 45
46 @click.command() 46 @click.command()
47 @click.argument('alignment_path', type=click.Path(exists=True)) 47 @click.argument('alignment_path', type=click.Path(exists=True))
48 @click.option('--minimum_size', default=18, type=int, help="Minimum readlength to consider") 48 @click.option('--minimum_size', default=18, type=int, help="Minimum readlength to consider")