oggmap plaza2orthomap -h
usage: oggmap <sub-command> plaza2orthomap [-h] [-qt QT] [-sl SL] [-og OG] [-out OUT] [-overwrite OVERWRITE]
optional arguments:
-h, --help show this help message and exit
-qt QT query species taxID (e.g. use <oggmap qlin -h> to get taxID)
-sl SL specify PLAZA species information file <species_information.csv>
-og OG specify PLAZA gene family file <genefamily_data.ORTHOFAM.csv> or genefamily_data.HOMFAM.csv
-out OUT specify output file <orthomap.tsv> (default: orthomap.tsv)
-overwrite OVERWRITE specify if existing output file should be overwritten (default: True)
plaza2orthomap example:
# using Orthologous gene family
$ plaza2orthomap -qt 3702 \
-sl species_information.csv \
-og genefamily_data.ORTHOFAM.csv \
-out 3702.orthofam.orthomap
# using Homologous gene family
$ plaza2orthomap -qt 3702 \
-sl species_information.csv \
-og genefamily_data.HOMFAM.csv \
-out 3702.homfam.orthomap