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Cleaner handling of reverse quality columns

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This commit is contained in:
Celine Mercier
2020-01-18 19:28:12 +01:00
parent ced82c4242
commit b4b2e62195
8 changed files with 85 additions and 46 deletions
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10
python/obitools3/commands/alignpairedend.pyx
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@ -14,7 +14,7 @@ from obitools3.libalign._qsrassemble import QSolexaRightReverseAssemble
from obitools3.libalign._solexapairend import buildConsensus, buildJoinedSequence
from obitools3.dms.obiseq cimport Nuc_Seq
from obitools3.libalign.shifted_ali cimport Kmer_similarity, Ali_shifted
from obitools3.commands.ngsfilter import REVERSE_SEQ_COLUMN_NAME, REVERSE_QUALITY_COLUMN_NAME
from obitools3.dms.capi.obiview cimport REVERSE_SEQUENCE_COLUMN, REVERSE_QUALITY_COLUMN
import sys
import os
@ -102,7 +102,7 @@ def alignmentIterator(entries, aligner):
seqR = reverse[i]
else:
seqF = Nuc_Seq.new_from_stored(entries[i])
seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQ_COLUMN_NAME], quality=seqF[REVERSE_QUALITY_COLUMN_NAME])
seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQUENCE_COLUMN], quality=seqF[REVERSE_QUALITY_COLUMN])
seqR.index = i
ali = aligner(seqF, seqR)
@ -196,8 +196,8 @@ def run(config):
reversed_column=None)
else:
aligner = Kmer_similarity(entries, \
column2=entries[REVERSE_SEQ_COLUMN_NAME], \
qual_column2=entries[REVERSE_QUALITY_COLUMN_NAME], \
column2=entries[REVERSE_SEQUENCE_COLUMN], \
qual_column2=entries[REVERSE_QUALITY_COLUMN], \
kmer_size=config['alignpairedend']['kmersize'], \
reversed_column=entries[b'reversed']) # column created by the ngsfilter tool
@ -221,7 +221,7 @@ def run(config):
buildConsensus(ali, consensus, seqF)
else:
if not two_views:
seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQ_COLUMN_NAME], quality = seqF[REVERSE_QUALITY_COLUMN_NAME])
seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQUENCE_COLUMN], quality = seqF[REVERSE_QUALITY_COLUMN])
else:
seqR = reverse[i]
buildJoinedSequence(ali, seqR, consensus, forward=seqF)