verkkofillet.pp.naming_contigs

verkkofillet.pp.naming_contigs(obj, node_database, duplicate_nodes, dam='mat', sire='pat', fai='assembly.fasta.fai')

Rename the contigs based on the provided chromosome map file.

Parameters:

• obj – The VerkkoFillet object to be used.

• node_database – The DataFrame containing the mapping of nodes to chromosomes.

• duplicate_nodes – List of duplicated nodes.

• gfa – The path to the GFA file. Default is “assembly.homopolymer-compressed.noseq.gfa”.

• dam – The name of the dam. Default is “mat”.

• sire – The name of the sire. Default is “pat”.

• fai – The path to the FASTA index file. Default is “assembly.fasta.fai”.

Returns:

The DataFrame containing the nodes and their corresponding assigned contig names.