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ngsfilter and alignpairedend: paired-end reads are now correctly

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reversed and labeled to be aligned correctly by alignpairedend
This commit is contained in:
Celine Mercier
2019-07-23 18:56:51 +02:00
parent 1759302829
commit d99702f56f
7 changed files with 39 additions and 5 deletions
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11
python/obitools3/commands/alignpairedend.pyx
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@ -188,9 +188,16 @@ def run(config):
if type(entries) == list:
forward = entries[0]
reverse = entries[1]
aligner = Kmer_similarity(forward, view2=reverse, kmer_size=config['alignpairedend']['kmersize'])
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'])
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)

5
python/obitools3/commands/ngsfilter.pyx
View File

@ -400,6 +400,8 @@ cdef tuple annotate(sequences, infos, verbose=False):
final_sequence = final_sequence[0:reversematch[1][1]]
else:
cut_seq = sequenceR[reversematch[1][2]:]
if not directmatch[0].forward:
cut_seq = cut_seq.reverse_complement
final_sequence[REVERSE_SEQ_COLUMN_NAME] = cut_seq.seq # used by alignpairedend tool
final_sequence[REVERSE_QUALITY_COLUMN_NAME] = cut_seq.quality # used by alignpairedend tool
@ -422,8 +424,9 @@ cdef tuple annotate(sequences, infos, verbose=False):
samples = infos[reversematch[3]]
if not directmatch[0].forward and not not_aligned: # don't reverse complement if not_aligned
if not directmatch[0].forward:
final_sequence = final_sequence.reverse_complement
final_sequence[b'reversed'] = True # used by the alignpairedend tool (in kmer_similarity.c)
sample=None