verkkofillet.tl.convertRefName

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verkkofillet.tl.convertRefName#

verkkofillet.tl.convertRefName(fasta, map_file, out_fasta=None, showOnly=False)[source]#

Replace the name in the given FASTA file.

Parameters:

  • fasta – FASTA file in which the contig name is to be replaced

  • map_file – A two-column file, delimited by tabs, containing the old and new contig names.

  • showOnly – If set to True, the script will not be executed; it will only display the intended operations. [default : False]

Returns:

Output fasta file with the new contig names.

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