verkkofillet.tl.mapBetweenNodes

verkkofillet.tl.mapBetweenNodes#

verkkofillet.tl.mapBetweenNodes(ref='assembly.homopolymer-compressed.fasta', query='assembly.homopolymer-compressed.fasta', threads=1, out=None, showOnly=False, working_directory='chromosome_assignment')[source]#

Map the query sequences to the reference sequences using mashmap.

Parameters:

  • ref – Path to the reference fasta file. [default: assembly.homopolymer-compressed.fasta]

  • query – Path to the query fasta file. [default: assembly.homopolymer-compressed.fasta]

  • threads – Number of threads to use. [default: 1]

  • out – Path to the output file. If not provided, the output file will be named automatically. [default: None]

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

  • working_directory – Path to the working directory. [default: chromosome_assignment]

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