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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
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@ -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

1
python/obitools3/dms/capi/kmer_similarity.pxd
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@ -34,6 +34,7 @@ cdef extern from "kmer_similarity.h" nogil:
index_t elt_idx2,
OBIDMS_column_p qual_col1,
OBIDMS_column_p qual_col2,
OBIDMS_column_p reversed_col,
uint8_t kmer_size,
int32_t** kmer_pos_array,
int32_t* kmer_pos_array_height_p,

1
python/obitools3/libalign/shifted_ali.pxd
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@ -28,5 +28,6 @@ cdef class Kmer_similarity:
cdef Obiview_p view2_p
cdef OBIDMS_column_p column2_p
cdef OBIDMS_column_p qual_col2_p
cdef OBIDMS_column_p reversed_col_p
cdef bint build_consensus
cpdef free(self)

9
python/obitools3/libalign/shifted_ali.pyx
View File

@ -56,7 +56,9 @@ cdef class Ali_shifted:
cdef class Kmer_similarity:
def __init__(self, View_NUC_SEQS view1, Column column1=None, Column qual_column1=None, View_NUC_SEQS view2=None, Column column2=None, Column qual_column2=None, uint8_t kmer_size=3, build_consensus=True) :
def __init__(self, View_NUC_SEQS view1, Column column1=None, Column qual_column1=None, \
View_NUC_SEQS view2=None, Column column2=None, Column qual_column2=None, \
uint8_t kmer_size=3, bint build_consensus=True, Column reversed_column=None) :
cdef Column default_seq_col
cdef Column default_qual_col
if kmer_size < 1 or kmer_size > 3:
@ -103,6 +105,10 @@ cdef class Kmer_similarity:
raise Exception("Kmer similarity with no quality column given must be given a NUC_SEQS view")
default_qual_col = view2[QUALITY_COLUMN]
self.qual_col2_p = default_qual_col.pointer()
if reversed_column is None:
self.reversed_col_p = NULL
else:
self.reversed_col_p = reversed_column.pointer()
def __call__(self, object seq1, object seq2):
@ -111,6 +117,7 @@ cdef class Kmer_similarity:
ali_p = kmer_similarity(self.view1_p, self.column1_p, seq1.index, 0, \
self.view2_p, self.column2_p, seq2.index, 0, \
self.qual_col1_p, self.qual_col2_p, \
self.reversed_col_p, \
self.kmer_size, \
&(self.kmer_pos_array_p), self.kmer_pos_array_height_a, \
&(self.shift_array_p), self.shift_array_height_a, \

11
src/kmer_similarity.c
View File

@ -65,7 +65,7 @@ void obi_free_shifted_ali(Obi_ali_p ali)
Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1, index_t elt_idx1,
Obiview_p view2, OBIDMS_column_p column2, index_t idx2, index_t elt_idx2,
OBIDMS_column_p qual_col1, OBIDMS_column_p qual_col2,
OBIDMS_column_p qual_col1, OBIDMS_column_p qual_col2, OBIDMS_column_p reversed_column,
uint8_t kmer_size,
int32_t** kmer_pos_array_p, int32_t* kmer_pos_array_height_p,
int32_t** shift_array_p, int32_t* shift_array_height_p,
@ -78,6 +78,7 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
Obi_ali_p ali = NULL;
int i, j;
bool switched_seqs;
bool reversed;
int score = 0;
Obi_blob_p blob1 = NULL;
Obi_blob_p blob2 = NULL;
@ -189,6 +190,14 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
seq2 = reverse_complement_sequence(seq2);
blob2 = obi_seq_to_blob(seq2);
// Check if the sequences have been reverse-complemented by the ngsfilter tool
if (reversed_column != NULL)
reversed = obi_get_bool_with_elt_idx_and_col_p_in_view(view1, reversed_column, idx1, 0); // assuming that reversed_column is in view1 is dirty but faster
else
reversed = false;
if (reversed)
switched_seqs = !switched_seqs;
// Save total length for the shift counts array
total_len = len1 + len2 + 1; // +1 for shift 0

6
src/kmer_similarity.h
View File

@ -78,6 +78,11 @@ void obi_free_shifted_ali(Obi_ali_p ali);
* @param column2 A pointer on the column containing the second sequence.
* @param idx2 The index of the second sequence in view2.
* @param elt_idx2 The element index of the second sequence in column2.
* @param qual_col1 A pointer on the column containing the quality associated with the first sequence (in view1).
* @param qual_col2 A pointer on the column containing the quality associated with the second sequence (in view2).
* @param reversed_column A pointer on the column containing a boolean indicating whether the sequences correspond
* to paired-end reads that might have been reversed before aligning them
* (e.g. when the ngsfilter tool is used before alignpairedend).
* @param kmer_size The kmer length to use. Must be >= 1 <= 4.
* @param kmer_pos_array The array used to store kmer positions. If NULL, allocated by the function.
* If needed, reallocated to a bigger size.
@ -109,6 +114,7 @@ Obi_ali_p kmer_similarity(Obiview_p view1,
index_t elt_idx2,
OBIDMS_column_p qual_col1,
OBIDMS_column_p qual_col2,
OBIDMS_column_p reversed_column,
uint8_t kmer_size,
int32_t** kmer_pos_array_p,
int32_t* kmer_pos_array_height_p,