verkkofillet.tl.renameContig#
- verkkofillet.tl.renameContig(obj, chrMap, out_mapFile='assembly.final.mapNaming.txt', original_fasta='assembly.fasta', output_fasta=None, showOnly=False)[source]#
Rename the contigs in the FASTA file based on the provided chromosome map file.
- Parameters:
obj – The VerkkoFillet object to be used.
chrMap – The DataFrame containing the mapping of old chromosome names to new chromosome names.
out_mapFile – The output file to save the chromosome map. Default is “assembly.final.mapNaming.txt”.
original_fasta – The path to the original FASTA file. Default is “assembly.fasta”.
output_fasta – The path to save the renamed FASTA file. If None, it will be generated with a suffix of “_rename.fasta”.
showOnly – If True, the command will be printed but not executed. Default is False.
- Returns:
output_fasta