verkkofillet.tl.showPairwiseAlign

verkkofillet.tl.showPairwiseAlign#

verkkofillet.tl.showPairwiseAlign(obj, size='large', working_directory='chromosome_assignment', mashmap_out='chromosome_assignment/assembly.mashmap.out', prefix='refAlign', idx=0.99, minLen=50000, showOnly=False)[source]#

Generate a dot plot from the mashmap output.

Parameters:

  • obj – An object that contains a .stats attribute, which should be a pandas DataFrame.

  • size (str) – Size of the image.

  • mashmap_out (str) – Path to the mashmap output file.

  • prefix (str) – Prefix for the output files.

  • idx (float) – Identity threshold for filtering alignments.

  • minLen (int) – Minimum length of alignments to be considered.

  • showOnly (bool) – If set to True, the script will not be executed; it will only display the intended operations.

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