verkkofillet.tl.runTrimming

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verkkofillet.tl.runTrimming#

verkkofillet.tl.runTrimming(obj, trim_contig_dict, original_fasta='assembly.fasta', trim_bed='internal_telomere/assembly.fasta.trim.bed', output_fasta=None, force=False)[source]#

Trim the contigs based on the provided coordinates.

Parameters:

  • obj – The VerkkoFillet object to be used.

  • trim_contig_dict – Dictionary containing contig names and their corresponding trim coordinates.

  • original_fasta – The path to the original assembly.fasta file. Default is “assembly.fasta”.

  • trim_bed – The path to the BED file containing trim coordinates. Default is “internal_telomere/assembly.fasta.trim.bed”.

  • output_fasta – The path to the output trimmed FASTA file. Default is None, which will generate a new file name based on the original FASTA file.

Returns:

The path to the trimmed FASTA file.

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