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Python API: small option improvements

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This commit is contained in:
Celine Mercier
2019-09-21 12:08:36 +02:00
parent 9e72c8d16a
commit f0f7edf152
3 changed files with 18 additions and 7 deletions
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9
python/obitools3/apps/optiongroups/__init__.py
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@ -222,8 +222,11 @@ def __addDMSOutputOption(optionManager):
group.add_argument('--no-create-dms', group.add_argument('--no-create-dms',
action="store_true", dest="obi:nocreatedms", action="store_true", dest="obi:nocreatedms",
default=False, default=False,
help="Don't create an output DMS is it is not existing") help="Don't create an output DMS it does not already exist")
def __addEltLimitOption(optionManager):
group = optionManager.add_argument_group("Option to limit the number of elements per line in columns")
group.add_argument('--max-elts', group.add_argument('--max-elts',
action="store", dest="obi:maxelts", action="store", dest="obi:maxelts",
metavar='<N>', metavar='<N>',
@ -306,3 +309,7 @@ def addAllOutputOption(optionManager):
def addNoProgressBarOption(optionManager): def addNoProgressBarOption(optionManager):
__addNoProgressBarOption(optionManager) __addNoProgressBarOption(optionManager)
def addEltLimitOption(optionManager):
__addEltLimitOption(optionManager)

10
python/obitools3/commands/alignpairedend.pyx
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@ -45,17 +45,17 @@ def addOptions(parser):
type=float, type=float,
help="Minimum score for keeping alignments") help="Minimum score for keeping alignments")
group.add_argument('-A', '--true-ali', # group.add_argument('-A', '--true-ali',
action="store_true", dest="alignpairedend:trueali", # action="store_true", dest="alignpairedend:trueali",
default=False, # default=False,
help="Performs gap free end alignment of sequences instead of using kmers to compute alignments (slower).") # help="Performs gap free end alignment of sequences instead of using kmers to compute alignments (slower).")
group.add_argument('-k', '--kmer-size', group.add_argument('-k', '--kmer-size',
action="store", dest="alignpairedend:kmersize", action="store", dest="alignpairedend:kmersize",
metavar="#", metavar="#",
default=3, default=3,
type=int, type=int,
help="K-mer size for kmer comparisons, between 1 and 4 (not when using -A option; default: 3)") help="K-mer size for kmer comparisons, between 1 and 4 (default: 3)")
la = QSolexaReverseAssemble() la = QSolexaReverseAssemble()

6
python/obitools3/commands/uniq.pyx
View File

@ -10,7 +10,10 @@ from obitools3.dms.column.column cimport Column, Column_line
from obitools3.dms.capi.obiview cimport QUALITY_COLUMN, COUNT_COLUMN, NUC_SEQUENCE_COLUMN, ID_COLUMN, TAXID_COLUMN, \ from obitools3.dms.capi.obiview cimport QUALITY_COLUMN, COUNT_COLUMN, NUC_SEQUENCE_COLUMN, ID_COLUMN, TAXID_COLUMN, \
TAXID_DIST_COLUMN, MERGED_TAXID_COLUMN, MERGED_COLUMN, MERGED_PREFIX TAXID_DIST_COLUMN, MERGED_TAXID_COLUMN, MERGED_COLUMN, MERGED_PREFIX
from obitools3.dms.capi.obitypes cimport OBI_INT, OBI_STR, index_t from obitools3.dms.capi.obitypes cimport OBI_INT, OBI_STR, index_t
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addTaxonomyOption from obitools3.apps.optiongroups import addMinimalInputOption, \
addMinimalOutputOption, \
addTaxonomyOption, \
addEltLimitOption
from obitools3.uri.decode import open_uri from obitools3.uri.decode import open_uri
from obitools3.apps.config import logger from obitools3.apps.config import logger
from obitools3.utils cimport tobytes, tostr from obitools3.utils cimport tobytes, tostr
@ -27,6 +30,7 @@ def addOptions(parser):
addMinimalInputOption(parser) addMinimalInputOption(parser)
addTaxonomyOption(parser) addTaxonomyOption(parser)
addMinimalOutputOption(parser) addMinimalOutputOption(parser)
addEltLimitOption(parser)
group = parser.add_argument_group('obi uniq specific options') group = parser.add_argument_group('obi uniq specific options')