oggmap orthomcl2orthomap -h
usage: oggmap <sub-command> orthomcl2orthomap [-h] [-tla TLA] [-sl SL] [-og OG] [-out OUT] [-overwrite OVERWRITE] [-dbname DBNAME]
options:
-h, --help show this help message and exit
-tla TLA query species orthomcl short name (THREE_LETTER_ABBREV)
-sl SL specify orthomcl species information file <genomeSummary_OrthoMCL-6.16.txt>
-og OG specify orthomcl groups file <groups_OrthoMCL-6.16.txt>
-out OUT specify output file <orthomap.tsv> (default: orthomap.tsv)
-overwrite OVERWRITE specify if existing output file should be overwritten (default: True)
-dbname DBNAME taxadb.sqlite file
orthomcl2orthomap example:
# download OrthoMCL DB data:
$ wget https://beta.orthomcl.org/common/downloads/release-6.21/genomeSummary_OrthoMCL-6.21.txt.gz
$ gunzip genomeSummary_OrthoMCL-6.21.txt.gz
$ wget https://beta.orthomcl.org/common/downloads/release-6.21/groups_OrthoMCL-6.21.txt.gz
$ gunzip groups_OrthoMCL-6.21.txt.gz
# quickly find 'Arabidopsis thaliana' short name
# grep 'Arabidopsis thaliana' genomeSummary_OrthoMCL-6.21.txt
# extract orthomap:
$ orthomcl2orthomap -tla atha \
-sl genomeSummary_OrthoMCL-6.21.txt \
-og groups_OrthoMCL-6.21.txt \
-out atha.orthomap \
-dbname taxadb.sqlite