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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.libalign._solexapairend import buildConsensus, buildJoinedSequence
from obitools3.dms.obiseq cimport Nuc_Seq from obitools3.dms.obiseq cimport Nuc_Seq
from obitools3.libalign.shifted_ali cimport Kmer_similarity, Ali_shifted 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 sys
import os import os
@ -102,7 +102,7 @@ def alignmentIterator(entries, aligner):
seqR = reverse[i] seqR = reverse[i]
else: else:
seqF = Nuc_Seq.new_from_stored(entries[i]) 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 seqR.index = i
ali = aligner(seqF, seqR) ali = aligner(seqF, seqR)
@ -196,8 +196,8 @@ def run(config):
reversed_column=None) reversed_column=None)
else: else:
aligner = Kmer_similarity(entries, \ aligner = Kmer_similarity(entries, \
column2=entries[REVERSE_SEQ_COLUMN_NAME], \ column2=entries[REVERSE_SEQUENCE_COLUMN], \
qual_column2=entries[REVERSE_QUALITY_COLUMN_NAME], \ qual_column2=entries[REVERSE_QUALITY_COLUMN], \
kmer_size=config['alignpairedend']['kmersize'], \ kmer_size=config['alignpairedend']['kmersize'], \
reversed_column=entries[b'reversed']) # column created by the ngsfilter tool reversed_column=entries[b'reversed']) # column created by the ngsfilter tool
@ -221,7 +221,7 @@ def run(config):
buildConsensus(ali, consensus, seqF) buildConsensus(ali, consensus, seqF)
else: else:
if not two_views: 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: else:
seqR = reverse[i] seqR = reverse[i]
buildJoinedSequence(ali, seqR, consensus, forward=seqF) buildJoinedSequence(ali, seqR, consensus, forward=seqF)

34
python/obitools3/commands/cat.pyx
View File

@ -2,15 +2,18 @@
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.dms import DMS from obitools3.dms import DMS
from obitools3.dms.view.view cimport View, Line_selection from obitools3.dms.view.view cimport View
from obitools3.uri.decode import open_uri from obitools3.uri.decode import open_uri
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption from obitools3.apps.optiongroups import addMinimalOutputOption
from obitools3.dms.view import RollbackException from obitools3.dms.view import RollbackException
from obitools3.apps.config import logger from obitools3.apps.config import logger
from obitools3.utils cimport str2bytes from obitools3.utils cimport str2bytes
from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
from obitools3.dms.capi.obiview cimport QUALITY_COLUMN from obitools3.dms.view.view cimport View
from obitools3.commands.ngsfilter import REVERSE_QUALITY_COLUMN_NAME # TODO should be stored in C from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, REVERSE_SEQUENCE_COLUMN, \
QUALITY_COLUMN, REVERSE_QUALITY_COLUMN
from obitools3.dms.capi.obitypes cimport OBI_SEQ, OBI_QUAL
from obitools3.dms.column.column cimport Column
import time import time
import sys import sys
@ -47,6 +50,8 @@ def run(config):
iview_list = [] iview_list = []
idms_list = [] idms_list = []
total_len = 0 total_len = 0
remove_qual = False
remove_rev_qual = False
v_type = View_NUC_SEQS v_type = View_NUC_SEQS
for v_uri in config["cat"]["views_to_cat"]: for v_uri in config["cat"]["views_to_cat"]:
input = open_uri(v_uri) input = open_uri(v_uri)
@ -56,6 +61,10 @@ def run(config):
i_view = input[1] i_view = input[1]
if input[2] != View_NUC_SEQS: # Check view type (output view is nuc_seqs view if all input view are nuc_seqs view) if input[2] != View_NUC_SEQS: # Check view type (output view is nuc_seqs view if all input view are nuc_seqs view)
v_type = View v_type = View
if QUALITY_COLUMN not in i_view: # Check if keep quality column in output view (if all input views have it)
remove_qual = True
if REVERSE_QUALITY_COLUMN not in i_view: # same as above for reverse quality
remove_rev_qual = True
total_len += len(i_view) total_len += len(i_view)
iview_list.append(i_view) iview_list.append(i_view)
idms_list.append(i_dms) idms_list.append(i_dms)
@ -69,6 +78,15 @@ def run(config):
o_dms = output[0] o_dms = output[0]
o_view = output[1] o_view = output[1]
# Initialize quality columns and their associated sequence columns if needed
if not remove_qual:
if NUC_SEQUENCE_COLUMN not in o_view:
Column.new_column(o_view, NUC_SEQUENCE_COLUMN, OBI_SEQ)
Column.new_column(o_view, QUALITY_COLUMN, OBI_QUAL, associated_column_name=NUC_SEQUENCE_COLUMN, associated_column_version=o_view[NUC_SEQUENCE_COLUMN].version)
if not remove_rev_qual:
Column.new_column(o_view, REVERSE_SEQUENCE_COLUMN, OBI_SEQ)
Column.new_column(o_view, REVERSE_QUALITY_COLUMN, OBI_QUAL, associated_column_name=REVERSE_SEQUENCE_COLUMN, associated_column_version=o_view[REVERSE_SEQUENCE_COLUMN].version)
# Initialize the progress bar # Initialize the progress bar
pb = ProgressBar(total_len, config, seconde=5) pb = ProgressBar(total_len, config, seconde=5)
@ -80,11 +98,11 @@ def run(config):
o_view[i] = l o_view[i] = l
i+=1 i+=1
# Deletes quality columns if there are any # Deletes quality columns if needed
if QUALITY_COLUMN in o_view: if QUALITY_COLUMN in o_view and remove_qual :
o_view.delete_column(QUALITY_COLUMN) o_view.delete_column(QUALITY_COLUMN)
if REVERSE_QUALITY_COLUMN_NAME in o_view: if REVERSE_QUALITY_COLUMN in o_view and remove_rev_qual :
o_view.delete_column(REVERSE_QUALITY_COLUMN_NAME) o_view.delete_column(REVERSE_QUALITY_COLUMN)
pb(i, force=True) pb(i, force=True)
print("", file=sys.stderr) print("", file=sys.stderr)

37
python/obitools3/commands/ngsfilter.pyx
View File

@ -13,6 +13,7 @@ from obitools3.libalign.apat_pattern import Primer_search
from obitools3.dms.obiseq cimport Nuc_Seq from obitools3.dms.obiseq cimport Nuc_Seq
from obitools3.dms.capi.obitypes cimport OBI_SEQ, OBI_QUAL from obitools3.dms.capi.obitypes cimport OBI_SEQ, OBI_QUAL
from obitools3.dms.capi.apat cimport MAX_PATTERN from obitools3.dms.capi.apat cimport MAX_PATTERN
from obitools3.dms.capi.obiview cimport REVERSE_SEQUENCE_COLUMN, REVERSE_QUALITY_COLUMN
from obitools3.utils cimport tobytes from obitools3.utils cimport tobytes
from libc.stdint cimport INT32_MAX from libc.stdint cimport INT32_MAX
@ -22,8 +23,8 @@ import sys
from cpython.exc cimport PyErr_CheckSignals from cpython.exc cimport PyErr_CheckSignals
REVERSE_SEQ_COLUMN_NAME = b"REVERSE_SEQUENCE" # used by alignpairedend tool #REVERSE_SEQ_COLUMN_NAME = b"REVERSE_SEQUENCE" # used by alignpairedend tool
REVERSE_QUALITY_COLUMN_NAME = b"REVERSE_QUALITY" # used by alignpairedend tool #REVERSE_QUALITY_COLUMN_NAME = b"REVERSE_QUALITY" # used by alignpairedend tool
__title__="Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers" __title__="Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers"
@ -259,8 +260,8 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
if not_aligned: if not_aligned:
sequences[1] = sequences[1].clone() sequences[1] = sequences[1].clone()
sequences[0][REVERSE_SEQ_COLUMN_NAME] = sequences[1].seq # used by alignpairedend tool sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq # used by alignpairedend tool
sequences[0][REVERSE_QUALITY_COLUMN_NAME] = sequences[1].quality # used by alignpairedend tool sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality # used by alignpairedend tool
for seq in sequences: for seq in sequences:
if hasattr(seq, "quality_array"): if hasattr(seq, "quality_array"):
@ -295,8 +296,8 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
if directmatch is None: if directmatch is None:
if not_aligned: if not_aligned:
sequences[0][REVERSE_SEQ_COLUMN_NAME] = sequences[1].seq # used by alignpairedend tool sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq # used by alignpairedend tool
sequences[0][REVERSE_QUALITY_COLUMN_NAME] = sequences[1].quality # used by alignpairedend tool sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality # used by alignpairedend tool
sequences[0][b'error']=b'No primer match' sequences[0][b'error']=b'No primer match'
return False, sequences[0] return False, sequences[0]
@ -314,8 +315,8 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
sequences[0] = sequences[0][directmatch[1][2]:] sequences[0] = sequences[0][directmatch[1][2]:]
else: else:
sequences[1] = sequences[1][directmatch[1][2]:] sequences[1] = sequences[1][directmatch[1][2]:]
sequences[0][REVERSE_SEQ_COLUMN_NAME] = sequences[1].seq # used by alignpairedend tool sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq # used by alignpairedend tool
sequences[0][REVERSE_QUALITY_COLUMN_NAME] = sequences[1].quality # used by alignpairedend tool sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality # used by alignpairedend tool
if directmatch[0].forward: if directmatch[0].forward:
sequences[0][b'direction']=b'forward' sequences[0][b'direction']=b'forward'
@ -361,8 +362,8 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
sequences[0] = sequences[0][:r[1]] sequences[0] = sequences[0][:r[1]]
else: else:
sequences[1] = sequences[1][:r[1]] sequences[1] = sequences[1][:r[1]]
sequences[0][REVERSE_SEQ_COLUMN_NAME] = sequences[1].seq # used by alignpairedend tool sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq # used by alignpairedend tool
sequences[0][REVERSE_QUALITY_COLUMN_NAME] = sequences[1].quality # used by alignpairedend tool sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality # used by alignpairedend tool
# do the same on the other seq # do the same on the other seq
if first_match_first_seq: if first_match_first_seq:
r = direct_primer.revcomp(sequences[1]) r = direct_primer.revcomp(sequences[1])
@ -373,8 +374,8 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
sequences[1] = sequences[1][:r[1]] sequences[1] = sequences[1][:r[1]]
else: else:
sequences[0] = sequences[0][:r[1]] sequences[0] = sequences[0][:r[1]]
sequences[0][REVERSE_SEQ_COLUMN_NAME] = sequences[1].seq sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq
sequences[0][REVERSE_QUALITY_COLUMN_NAME] = sequences[1].quality sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality
# Look for other primer in the other direction on the sequence, or # Look for other primer in the other direction on the sequence, or
@ -442,8 +443,8 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
sequences[1] = sequences[1][reversematch[1][2]:] sequences[1] = sequences[1][reversematch[1][2]:]
if not directmatch[0].forward: if not directmatch[0].forward:
sequences[1] = sequences[1].reverse_complement sequences[1] = sequences[1].reverse_complement
sequences[0][REVERSE_SEQ_COLUMN_NAME] = sequences[1].seq # used by alignpairedend tool sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq # used by alignpairedend tool
sequences[0][REVERSE_QUALITY_COLUMN_NAME] = sequences[1].quality # used by alignpairedend tool sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality # used by alignpairedend tool
else: else:
sequences[0] = sequences[0][reversematch[1][2]:] sequences[0] = sequences[0][reversematch[1][2]:]
@ -605,12 +606,12 @@ def run(config):
paired_p.revcomp.aligner = aligner paired_p.revcomp.aligner = aligner
if not_aligned: # create columns used by alignpairedend tool if not_aligned: # create columns used by alignpairedend tool
Column.new_column(o_view, REVERSE_SEQ_COLUMN_NAME, OBI_SEQ) Column.new_column(o_view, REVERSE_SEQUENCE_COLUMN, OBI_SEQ)
Column.new_column(o_view, REVERSE_QUALITY_COLUMN_NAME, OBI_QUAL, associated_column_name=REVERSE_SEQ_COLUMN_NAME, associated_column_version=o_view[REVERSE_SEQ_COLUMN_NAME].version) Column.new_column(o_view, REVERSE_QUALITY_COLUMN, OBI_QUAL, associated_column_name=REVERSE_SEQUENCE_COLUMN, associated_column_version=o_view[REVERSE_SEQUENCE_COLUMN].version)
if unidentified is not None: if unidentified is not None:
Column.new_column(unidentified, REVERSE_SEQ_COLUMN_NAME, OBI_SEQ) Column.new_column(unidentified, REVERSE_SEQUENCE_COLUMN, OBI_SEQ)
Column.new_column(unidentified, REVERSE_QUALITY_COLUMN_NAME, OBI_QUAL, associated_column_name=REVERSE_SEQ_COLUMN_NAME, associated_column_version=unidentified[REVERSE_SEQ_COLUMN_NAME].version) Column.new_column(unidentified, REVERSE_QUALITY_COLUMN, OBI_QUAL, associated_column_name=REVERSE_SEQUENCE_COLUMN, associated_column_version=unidentified[REVERSE_SEQUENCE_COLUMN].version)
g = 0 g = 0
u = 0 u = 0

10
python/obitools3/commands/uniq.pyx
View File

@ -8,7 +8,8 @@ from obitools3.dms.view import RollbackException
from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
from obitools3.dms.column.column cimport Column, Column_line from obitools3.dms.column.column cimport Column, Column_line
from obitools3.dms.capi.obiview cimport QUALITY_COLUMN, COUNT_COLUMN, NUC_SEQUENCE_COLUMN, ID_COLUMN, TAXID_COLUMN, \ from obitools3.dms.capi.obiview cimport QUALITY_COLUMN, COUNT_COLUMN, NUC_SEQUENCE_COLUMN, ID_COLUMN, TAXID_COLUMN, \
TAXID_DIST_COLUMN, MERGED_TAXID_COLUMN, MERGED_COLUMN, MERGED_PREFIX TAXID_DIST_COLUMN, MERGED_TAXID_COLUMN, MERGED_COLUMN, MERGED_PREFIX, \
REVERSE_QUALITY_COLUMN
from obitools3.dms.capi.obitypes cimport OBI_INT, OBI_STR, index_t from obitools3.dms.capi.obitypes cimport OBI_INT, OBI_STR, index_t
from obitools3.apps.optiongroups import addMinimalInputOption, \ from obitools3.apps.optiongroups import addMinimalInputOption, \
addMinimalOutputOption, \ addMinimalOutputOption, \
@ -25,9 +26,6 @@ from cpython.exc cimport PyErr_CheckSignals
__title__="Group sequence records together" __title__="Group sequence records together"
REVERSE_QUALITY_COLUMN_NAME = b"REVERSE_QUALITY" # TODO from ngsfilter, move to C
def addOptions(parser): def addOptions(parser):
addMinimalInputOption(parser) addMinimalInputOption(parser)
@ -496,8 +494,8 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
# Deletes quality columns if there is one because the matching between sequence and quality will be broken (quality set to NA when sequence not) # Deletes quality columns if there is one because the matching between sequence and quality will be broken (quality set to NA when sequence not)
if QUALITY_COLUMN in view: if QUALITY_COLUMN in view:
o_view.delete_column(QUALITY_COLUMN) o_view.delete_column(QUALITY_COLUMN)
if REVERSE_QUALITY_COLUMN_NAME in view: if REVERSE_QUALITY_COLUMN in view:
o_view.delete_column(REVERSE_QUALITY_COLUMN_NAME) o_view.delete_column(REVERSE_QUALITY_COLUMN)
if taxonomy is not None: if taxonomy is not None:
print("") # TODO because in the middle of progress bar. Better solution? print("") # TODO because in the middle of progress bar. Better solution?

2
python/obitools3/dms/capi/obiview.pxd
View File

@ -24,6 +24,8 @@ cdef extern from "obiview.h" nogil:
extern const_char_p ID_COLUMN extern const_char_p ID_COLUMN
extern const_char_p DEFINITION_COLUMN extern const_char_p DEFINITION_COLUMN
extern const_char_p QUALITY_COLUMN extern const_char_p QUALITY_COLUMN
extern const_char_p REVERSE_QUALITY_COLUMN
extern const_char_p REVERSE_SEQUENCE_COLUMN
extern const_char_p COUNT_COLUMN extern const_char_p COUNT_COLUMN
extern const_char_p TAXID_COLUMN extern const_char_p TAXID_COLUMN
extern const_char_p MERGED_TAXID_COLUMN extern const_char_p MERGED_TAXID_COLUMN

13
python/obitools3/dms/column/column.pyx
View File

@ -21,7 +21,11 @@ from ..capi.obiutils cimport obi_format_date
from ..capi.obiview cimport obi_view_add_column, \ from ..capi.obiview cimport obi_view_add_column, \
obi_view_get_pointer_on_column_in_view, \ obi_view_get_pointer_on_column_in_view, \
Obiview_p, \ Obiview_p, \
NUC_SEQUENCE_COLUMN NUC_SEQUENCE_COLUMN, \
QUALITY_COLUMN, \
REVERSE_SEQUENCE_COLUMN, \
REVERSE_QUALITY_COLUMN
from ..object cimport OBIDeactivatedInstanceError from ..object cimport OBIDeactivatedInstanceError
@ -122,11 +126,18 @@ cdef class Column(OBIWrapper) :
if data_type == OBI_QUAL: if data_type == OBI_QUAL:
if associated_column_name_b == b"": if associated_column_name_b == b"":
if column_name == QUALITY_COLUMN:
if NUC_SEQUENCE_COLUMN not in view: if NUC_SEQUENCE_COLUMN not in view:
raise RuntimeError("Cannot create column %s in view %s: trying to create quality column but no NUC_SEQ column to associate it with in the view" % (bytes2str(column_name_b), raise RuntimeError("Cannot create column %s in view %s: trying to create quality column but no NUC_SEQ column to associate it with in the view" % (bytes2str(column_name_b),
bytes2str(view.name))) bytes2str(view.name)))
associated_column_name_b = NUC_SEQUENCE_COLUMN associated_column_name_b = NUC_SEQUENCE_COLUMN
associated_column_version = view[NUC_SEQUENCE_COLUMN].version associated_column_version = view[NUC_SEQUENCE_COLUMN].version
elif column_name == REVERSE_QUALITY_COLUMN:
if REVERSE_SEQUENCE_COLUMN not in view:
raise RuntimeError("Cannot create column %s in view %s: trying to create reverse quality column but no REVERSE_SEQUENCE column to associate it with in the view" % (bytes2str(column_name_b),
bytes2str(view.name)))
associated_column_name_b = REVERSE_SEQUENCE_COLUMN
associated_column_version = view[REVERSE_SEQUENCE_COLUMN].version
if (obi_view_add_column(view = view.pointer(), if (obi_view_add_column(view = view.pointer(),
column_name = column_name_b, column_name = column_name_b,

6
python/obitools3/libalign/_solexapairend.pyx
View File

@ -6,6 +6,7 @@ from .solexapairend import iterOnAligment
from .shifted_ali cimport Ali_shifted from .shifted_ali cimport Ali_shifted
from obitools3.dms.capi.obiview cimport Obiview_p, QUALITY_COLUMN, NUC_SEQUENCE_COLUMN, \ from obitools3.dms.capi.obiview cimport Obiview_p, QUALITY_COLUMN, NUC_SEQUENCE_COLUMN, \
REVERSE_SEQUENCE_COLUMN, REVERSE_QUALITY_COLUMN, \
obi_set_qual_int_with_elt_idx_and_col_p_in_view, \ obi_set_qual_int_with_elt_idx_and_col_p_in_view, \
obi_set_str_with_elt_idx_and_col_p_in_view obi_set_str_with_elt_idx_and_col_p_in_view
@ -13,7 +14,6 @@ from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
from obitools3.dms.view.view cimport View from obitools3.dms.view.view cimport View
from obitools3.dms.column.column cimport Column from obitools3.dms.column.column cimport Column
from obitools3.commands.ngsfilter import REVERSE_SEQ_COLUMN_NAME, REVERSE_QUALITY_COLUMN_NAME
from math import log10 from math import log10
@ -233,7 +233,7 @@ def buildConsensus(ali, seq, ref_tags=None):
seq[b'mode']=b'alignment' seq[b'mode']=b'alignment'
for tag in ref_tags: for tag in ref_tags:
if tag != REVERSE_SEQ_COLUMN_NAME and tag != REVERSE_QUALITY_COLUMN_NAME and \ if tag != REVERSE_SEQUENCE_COLUMN and tag != REVERSE_QUALITY_COLUMN and \
tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN: tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN:
seq[tag] = ref_tags[tag] seq[tag] = ref_tags[tag]
@ -254,7 +254,7 @@ def buildJoinedSequence(ali, reverse, seq, forward=None):
seq[b"mode"]=b"joined" seq[b"mode"]=b"joined"
seq[b"pairedend_limit"]=len(forward) seq[b"pairedend_limit"]=len(forward)
for tag in forward: for tag in forward:
if tag != REVERSE_SEQ_COLUMN_NAME and tag != REVERSE_QUALITY_COLUMN_NAME: if tag != REVERSE_SEQUENCE_COLUMN and tag != REVERSE_QUALITY_COLUMN:
seq[tag] = forward[tag] seq[tag] = forward[tag]
return seq return seq

9
src/obiview.h
View File

@ -52,6 +52,15 @@
#define QUALITY_COLUMN "QUALITY" /**< The name of the column containing the sequence qualities #define QUALITY_COLUMN "QUALITY" /**< The name of the column containing the sequence qualities
* in NUC_SEQS_VIEW views. * in NUC_SEQS_VIEW views.
*/ */
#define REVERSE_QUALITY_COLUMN "REVERSE_QUALITY" /**< The name of the column containing the sequence qualities
* of the reverse read (generated by ngsfilter, used by alignpairedend).
*/
#define REVERSE_SEQUENCE_COLUMN "REVERSE_SEQUENCE" /**< The name of the column containing the sequence
* of the reverse read (generated by ngsfilter, used by alignpairedend).
*/
#define QUALITY_COLUMN "QUALITY" /**< The name of the column containing the sequence qualities
* in NUC_SEQS_VIEW views.
*/
#define COUNT_COLUMN "COUNT" /**< The name of the column containing the sequence counts #define COUNT_COLUMN "COUNT" /**< The name of the column containing the sequence counts
* in NUC_SEQS_VIEW views. * in NUC_SEQS_VIEW views.
*/ */