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Added atexit command to obi import, obi uniq and obi less

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This commit is contained in:
Celine Mercier
2017-10-16 11:09:55 +02:00
parent 04e065094a
commit 1ae634d56b
3 changed files with 14 additions and 13 deletions
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4
python/obitools3/commands/import.pyx
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@ -12,6 +12,7 @@ from obitools3.dms.view.view cimport View
from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
from obitools3.dms.column.column cimport Column from obitools3.dms.column.column cimport Column
from obitools3.dms.obiseq cimport Nuc_Seq from obitools3.dms.obiseq cimport Nuc_Seq
from obitools3.dms import DMS
from obitools3.utils cimport tobytes, \ from obitools3.utils cimport tobytes, \
get_obitype, \ get_obitype, \
@ -82,6 +83,7 @@ def run(config):
cdef bytes NA_value cdef bytes NA_value
global obi_errno global obi_errno
DMS.obi_atexit()
logger("info","obi import : imports file into an DMS") logger("info","obi import : imports file into an DMS")
@ -238,6 +240,6 @@ def run(config):
print("\n") print("\n")
print(view.__repr__()) print(view.__repr__())
input[0].close() # TODO input[0].close() # TODO ?
output[0].close() output[0].close()

3
python/obitools3/commands/less.pyx
View File

@ -2,6 +2,7 @@
from obitools3.apps.optiongroups import addSequenceInputOption from obitools3.apps.optiongroups import addSequenceInputOption
from obitools3.uri.decode import open_uri from obitools3.uri.decode import open_uri
from obitools3.dms import DMS
__title__="Less equivalent" __title__="Less equivalent"
@ -26,6 +27,8 @@ def run(config):
cdef object entries cdef object entries
cdef int n cdef int n
DMS.obi_atexit()
input = open_uri(config['obi']['inputURI']) input = open_uri(config['obi']['inputURI'])
entries = input[1] entries = input[1]

14
python/obitools3/commands/uniq.pyx
View File

@ -1,7 +1,7 @@
#cython: language_level=3 #cython: language_level=3
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.dms.dms cimport DMS from obitools3.dms import DMS
from obitools3.dms.view.view cimport View, Line from obitools3.dms.view.view cimport View, Line
from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
from obitools3.dms.column.column cimport Column, Column_line from obitools3.dms.column.column cimport Column, Column_line
@ -44,6 +44,7 @@ def addOptions(parser):
"used to group sequences before dereplication " "used to group sequences before dereplication "
"(option can be used several times).") "(option can be used several times).")
# TODO discuss
# group.add_argument('--prefix', '-p', # group.add_argument('--prefix', '-p',
# action="store_true", dest="uniq:prefix", # action="store_true", dest="uniq:prefix",
# default=False, # default=False,
@ -400,7 +401,6 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
merge_taxonomy_classification(o_view, taxonomy) merge_taxonomy_classification(o_view, taxonomy)
def run(config): def run(config):
cdef tuple input cdef tuple input
@ -411,6 +411,8 @@ def run(config):
cdef View_NUC_SEQS o_view cdef View_NUC_SEQS o_view
cdef ProgressBar pb cdef ProgressBar pb
DMS.obi_atexit()
logger("info","obi uniq") logger("info","obi uniq")
input = open_uri(config['obi']['inputURI']) input = open_uri(config['obi']['inputURI'])
@ -435,13 +437,7 @@ def run(config):
# Initialize the progress bar # Initialize the progress bar
pb = ProgressBar(len(entries), config, seconde=5) pb = ProgressBar(len(entries), config, seconde=5)
# TODO uniq_sequences(entries, o_view, pb, mergedKeys_list=config['uniq']['merge'], taxonomy=taxo, mergeIds=config['uniq']['mergeids'], categories=config['uniq']['categories'])
# if options.prefix:
# usm = uniqPrefixSequence
# else:
usm = uniq_sequences
usm(entries, o_view, pb, mergedKeys_list=config['uniq']['merge'], taxonomy=taxo, mergeIds=config['uniq']['mergeids'], categories=config['uniq']['categories'])
print("\n") print("\n")
print(repr(o_view)) print(repr(o_view))