obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

grep: added taxonomy check

Browse Source
This commit is contained in:
mercierc
2021-05-31 17:03:39 +12:00
parent 2156588ff6
commit 03c174fd7a
1 changed files with 7 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files

7
python/obitools3/commands/grep.pyx
View File

@ -258,6 +258,13 @@ def Filter_generator(options, tax_filter, i_view):
def Taxonomy_filter_generator(taxo, options): def Taxonomy_filter_generator(taxo, options):
if (("required_ranks" in options and options["required_ranks"]) or \
("required_taxids" in options and options["required_taxids"]) or \
("ignored_taxids" in options and options["ignored_taxids"])) and \
(taxo is None):
raise RollbackException("obi grep error: can't use taxonomy options without providing a taxonomy. Rollbacking view")
if taxo is not None: if taxo is not None:
def tax_filter(seq): def tax_filter(seq):
good = True good = True