verkkofillet.pp.mkCNSdir

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verkkofillet.pp.mkCNSdir#

verkkofillet.pp.mkCNSdir(obj, new_folder_path, final_gaf='assembly.fixed.paths.gaf', missingEdge=False, missing_edge_dir='missing_edge')[source]#

Creates a new CNS directory by creating symbolic links to the original verkko directory.

Parameters:

  • obj – Object containing the original verkko directory path.

  • new_folder_path – Path to the new folder to be created.

  • final_gaf – Path to the final GAF file. Default is “final_rukki_fixed.paths.gaf”.

  • missingEdge – Whether to handle missing edges. Default is False.

  • tmp_id – Path to the temporary ID file. Default is “missing_edge/ont_subset.tmp.id”.

  • tmp_fasta – Path to the temporary FASTA file. Default is “missing_edge/ont_subset.tmp.fasta”.

Returns:

new folder with mendatory files and symbolic links

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