verkkofillet.pl.showMashmapOri

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verkkofillet.pl.showMashmapOri#

verkkofillet.pl.showMashmapOri(obj, mashmap_out='chromosome_assignment/assembly.mashmap.out', by='chr_hap', width=5, height=7, save=True, figName=None, force=False)[source]#

Generates a bar plot showing the covered regions of the assembly for each reference.

Parameters:

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

  • mashmap_out – The Mashmap output file, aligning the assembly to the reference. Default is assembly.mashmap.out.filtered.out.

  • by – Specifies the grouping method for the plot. Default is “chr_hap”. Available options are [‘contig’, ‘all’, ‘chr_hap’].

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