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Minor fixes

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This commit is contained in:
Celine Mercier
2018-03-16 19:05:09 +01:00
parent d4f7e02c85
commit 9fb63d4894
2 changed files with 8 additions and 6 deletions
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6
python/obitools3/commands/alignpairedend.pyx
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@ -28,14 +28,14 @@ def addOptions(parser):
group.add_argument('-f', '--forward-reads', group.add_argument('-f', '--forward-reads',
action="store", dest="alignpairedend:forward", action="store", dest="alignpairedend:forward",
metavar="<FILENAME>", metavar="<URI>",
default=None, default=None,
type=str, type=str,
help="URI to the forward reads") help="URI to the forward reads")
group.add_argument('-r', '--reverse-reads', group.add_argument('-r', '--reverse-reads',
action="store", dest="alignpairedend:reverse", action="store", dest="alignpairedend:reverse",
metavar="<FILENAME>", metavar="<URI>",
default=None, default=None,
type=str, type=str,
help="URI to the reverse reads") help="URI to the reverse reads")
@ -56,6 +56,8 @@ def addOptions(parser):
help="Minimum score for keeping alignments") help="Minimum score for keeping alignments")
# TODO declarations, cdef, imports
la = QSolexaReverseAssemble() la = QSolexaReverseAssemble()
ra = QSolexaRightReverseAssemble() ra = QSolexaRightReverseAssemble()
def buildAlignment(Nuc_Seq_Stored direct, Nuc_Seq_Stored reverse): def buildAlignment(Nuc_Seq_Stored direct, Nuc_Seq_Stored reverse):

8
python/obitools3/commands/ngsfilter.pyx
View File

@ -5,16 +5,13 @@ from obitools3.dms import DMS
from obitools3.dms.view import RollbackException from obitools3.dms.view import RollbackException
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
from obitools3.dms.capi.obiview cimport QUALITY_COLUMN, COUNT_COLUMN, NUC_SEQUENCE_COLUMN, ID_COLUMN
from obitools3.dms.capi.obitypes cimport OBI_INT, OBI_STR, index_t, OBI_QUAL
from obitools3.apps.optiongroups import addSequenceInputOption, addMinimalOutputOption from obitools3.apps.optiongroups import addSequenceInputOption, addMinimalOutputOption
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.align._freeendgapfm import FreeEndGapFullMatch from obitools3.align._freeendgapfm import FreeEndGapFullMatch
from obitools3.dms.obiseq cimport Nuc_Seq, Nuc_Seq_Stored from obitools3.dms.obiseq cimport Nuc_Seq
from functools import reduce, cmp_to_key from functools import reduce, cmp_to_key
import math import math
from curses.ascii import SO
__title__="Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers" __title__="Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers"
@ -388,6 +385,9 @@ def run(config):
except Exception, e: except Exception, e:
raise RollbackException("obi ngsfilter error, rollbacking views: "+str(e), o_view, unidentified) raise RollbackException("obi ngsfilter error, rollbacking views: "+str(e), o_view, unidentified)
print("\n")
print(repr(o_view))
input[0].close() input[0].close()
output[0].close() output[0].close()
info_input[0].close() info_input[0].close()