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

Cython: rearranged input and output format options to have both and

Browse Source 
updated commands accordingly
This commit is contained in:
Celine Mercier
2018-10-17 11:19:48 +02:00
parent e6bbe13d81
commit 58589e04be
11 changed files with 120 additions and 77 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
python/obitools3/commands/annotate.pyx
View File

@ -4,7 +4,7 @@ from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.dms import DMS
from obitools3.dms.view.view cimport View, Line_selection
from obitools3.uri.decode import open_uri
from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyInputOption, addMinimalOutputOption
from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption
from obitools3.dms.view import RollbackException
from functools import reduce
from obitools3.apps.config import logger
@ -29,7 +29,7 @@ SPECIAL_COLUMNS = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_CO
def addOptions(parser):
addMinimalInputOption(parser)
addTaxonomyInputOption(parser)
addTaxonomyOption(parser)
addMinimalOutputOption(parser)
group=parser.add_argument_group('obi annotate specific options')