verkkofillet.tl.filterContigs

Contents

verkkofillet.tl.filterContigs#

verkkofillet.tl.filterContigs(mapfile, assembly, out_prefix=None, filter_chr_list=None, showOnly=False)[source]#

Filter the contigs in the FASTA file based on the provided list of contigs. For chromosome assignment, we recommend using the reference genome that contains only the chromosomes to which the contigs should be assigned.

Parameters:

  • mapfile – The path to the map file. The map file should contain the list of contigs to be filtered.

  • assembly – The path to the original FASTA file.

  • out_prefix – The prefix for the output file. If None, it will be generated based on the input file name with surfixed “_filtered.fa”.

  • filter_chr_list – The list of contigs to be filtered.

  • showOnly – If True, the command will be printed but not executed. Default is False.

Returns:

fasta file with filtered contigs

Contents