oggmap of2orthomap -h
usage: oggmap <sub-command> of2orthomap [-h] [-seqname SEQNAME] [-qt QT] [-sl SL] [-oc OC] [-og OG] [-out OUT]
[-overwrite OVERWRITE]
options:
-h, --help show this help message and exit
-seqname SEQNAME sequence name of the query species in orthofinder(see column names of <Orthogroups.tsv>)
-qt QT query species taxid (e.g. use <oggmap qlin -h> to get taxid)
-sl SL species list as <orthofinder name><tab><species taxid> (only samples in this list will be processed)
-oc OC specify orthofinder <Orthogroups.GeneCounts.tsv> (see Orthogroups directory)
-og OG specify orthofinder <Orthogroups.tsv> (see Orthogroups directory)
-out OUT specify output file <orthomap.tsv> (default: orthomap.tsv)
-overwrite OVERWRITE specify if existing output file should be overwritten (default: True)
of2orthomap example:
# download OrthoFinder example:
$ wget https://zenodo.org/record/7796253/files/ensembl_105_orthofinder_Orthogroups.GeneCount.tsv.zip
$ wget https://zenodo.org/record/7796253/files/ensembl_105_orthofinder_Orthogroups.tsv.zip
$ wget https://zenodo.org/record/7796253/files/ensembl_105_orthofinder_species_list.tsv
# extract orthomap:
$ of2orthomap -seqname Danio_rerio.GRCz11.cds.longest -qt 7955 \
-sl ensembl_105_orthofinder_species_list.tsv \
-oc ensembl_105_orthofinder_Orthogroups.GeneCount.tsv.zip \
-og ensembl_105_orthofinder_Orthogroups.tsv.zip