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Added signal catching and handling in C and Cython

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This commit is contained in:
Celine Mercier
2019-09-21 16:47:22 +02:00
parent 06f9d6da60
commit ec0737a600
23 changed files with 178 additions and 25 deletions
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40
python/obitools3/commands/alignpairedend.pyx
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@ -19,6 +19,7 @@ from obitools3.commands.ngsfilter import REVERSE_SEQ_COLUMN_NAME, REVERSE_QUALIT
import sys
import os
from cpython.exc cimport PyErr_CheckSignals
__title__="Aligns paired-ended reads"
@ -95,6 +96,7 @@ def alignmentIterator(entries, aligner):
entries_len = len(entries)
for i in range(entries_len):
if two_views:
seqF = forward[i]
seqR = reverse[i]
@ -180,24 +182,24 @@ def run(config):
# Initialize the progress bar
pb = ProgressBar(entries_len, config, seconde=5)
if config['alignpairedend']['trueali']:
kmer_ali = False
aligner = buildAlignment
else :
kmer_ali = True
if type(entries) == list:
forward = entries[0]
reverse = entries[1]
aligner = Kmer_similarity(forward, \
view2=reverse, \
kmer_size=config['alignpairedend']['kmersize'], \
reversed_column=None)
else:
aligner = Kmer_similarity(entries, \
column2=entries[REVERSE_SEQ_COLUMN_NAME], \
qual_column2=entries[REVERSE_QUALITY_COLUMN_NAME], \
kmer_size=config['alignpairedend']['kmersize'], \
reversed_column=entries[b'reversed']) # column created by the ngsfilter tool
#if config['alignpairedend']['trueali']:
# kmer_ali = False
# aligner = buildAlignment
#else :
kmer_ali = True
if type(entries) == list:
forward = entries[0]
reverse = entries[1]
aligner = Kmer_similarity(forward, \
view2=reverse, \
kmer_size=config['alignpairedend']['kmersize'], \
reversed_column=None)
else:
aligner = Kmer_similarity(entries, \
column2=entries[REVERSE_SEQ_COLUMN_NAME], \
qual_column2=entries[REVERSE_QUALITY_COLUMN_NAME], \
kmer_size=config['alignpairedend']['kmersize'], \
reversed_column=entries[b'reversed']) # column created by the ngsfilter tool
ba = alignmentIterator(entries, aligner)
@ -206,6 +208,8 @@ def run(config):
pb(i)
PyErr_CheckSignals()
consensus = view[i]
if not two_views: