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Fixed the new alignpaired end to work after ngsfilter with the 9879847

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Celine Mercier
2019-02-17 18:32:35 +01:00
parent 4ddd1a1c37
commit e026e9ec83
9 changed files with 151 additions and 83 deletions
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11
python/obitools3/commands/alignpairedend.pyx
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@ -15,16 +15,12 @@ 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
import sys
import os
REVERSE_SEQ_COLUMN_NAME = b"REVERSE_SEQUENCE"
REVERSE_QUALITY_COLUMN_NAME = b"REVERSE_QUALITY"
__title__="Aligns paired-ended reads"
@ -106,8 +102,7 @@ def alignmentIterator(entries, aligner):
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])
seqF.pop(REVERSE_SEQ_COLUMN_NAME)
seqF.pop(REVERSE_QUALITY_COLUMN_NAME)
seqR.index = i
ali = aligner(seqF, seqR)
@ -196,7 +191,7 @@ def run(config):
reverse = entries[1]
aligner = Kmer_similarity(forward, view2=reverse, kmer_size=config['alignpairedend']['kmersize'])
else:
aligner = Kmer_similarity(entries, kmer_size=config['alignpairedend']['kmersize'])
aligner = Kmer_similarity(entries, column2=entries[REVERSE_SEQ_COLUMN_NAME], qual_column2=entries[REVERSE_QUALITY_COLUMN_NAME], kmer_size=config['alignpairedend']['kmersize'])
ba = alignmentIterator(entries, aligner)