verkkofillet.tl.chrAssign#
- verkkofillet.tl.chrAssign(obj, ref, working_directory='chromosome_assignment', fasta='assembly.fasta', chr_name='chr', idx=99, showOnly=False, force=False)[source]#
Run the script to align the assembly to the given reference using mashmap and obtain the chromosome assignment results.
Parameters:#
- obj (verko-fillet object):
An object that contains a .stats attribute, which should be a pandas DataFrame.
- ref (str) :
Existing reference
- fasta (str):
verkko assembly. [default:
assembly.fasta]- working_directory (str):
output directory [default :
./stats/]- chr_name (str):
prefix of the chromosome name in the previous reference. [default : “chr”]
- idx (int):
Identity threshold to filter mashmap result [defualt : 99]
- showOnly (bool):
If set to True, the script will not be executed; it will only display the intended operations. [default : FALSE]
- force (bool):
If set to True, the script will overwrite the existing files. [default : FALSE]
Return:#
: {working_directory}/assembly.mashmap.out {working_directory}/assembly.mashmap.out.filtered.out {working_directory}/chr_completeness_max_hap1 {working_directory}/chr_completeness_max_hap2 {working_directory}/translation_hap1 {working_directory}/translation_hap2