256 lines
7.7 KiB
Cython
Executable File
256 lines
7.7 KiB
Cython
Executable File
#cython: language_level=3
|
|
|
|
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
|
|
from obitools3.dms import DMS
|
|
from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
|
|
from obitools3.dms.column.column cimport Column
|
|
from obitools3.dms.capi.obiview cimport QUALITY_COLUMN
|
|
from obitools3.dms.capi.obitypes cimport OBI_QUAL
|
|
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
|
|
from obitools3.uri.decode import open_uri
|
|
from obitools3.apps.config import logger
|
|
from obitools3.libalign._qsassemble import QSolexaReverseAssemble
|
|
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
|
|
|
|
from cpython.exc cimport PyErr_CheckSignals
|
|
|
|
__title__="Aligns paired-ended reads"
|
|
|
|
|
|
|
|
def addOptions(parser):
|
|
|
|
addMinimalInputOption(parser)
|
|
addMinimalOutputOption(parser)
|
|
|
|
group = parser.add_argument_group('obi alignpairedend specific options')
|
|
|
|
group.add_argument('-R', '--reverse-reads',
|
|
action="store", dest="alignpairedend:reverse",
|
|
metavar="<URI>",
|
|
default=None,
|
|
type=str,
|
|
help="URI to the reverse reads if they are in a different view than the forward reads")
|
|
|
|
group.add_argument('--score-min',
|
|
action="store", dest="alignpairedend:smin",
|
|
metavar="#.###",
|
|
default=None,
|
|
type=float,
|
|
help="Minimum score for keeping alignments")
|
|
|
|
# group.add_argument('-A', '--true-ali',
|
|
# action="store_true", dest="alignpairedend:trueali",
|
|
# default=False,
|
|
# help="Performs gap free end alignment of sequences instead of using kmers to compute alignments (slower).")
|
|
|
|
group.add_argument('-k', '--kmer-size',
|
|
action="store", dest="alignpairedend:kmersize",
|
|
metavar="#",
|
|
default=3,
|
|
type=int,
|
|
help="K-mer size for kmer comparisons, between 1 and 4 (default: 3)")
|
|
|
|
|
|
la = QSolexaReverseAssemble()
|
|
ra = QSolexaRightReverseAssemble()
|
|
cdef object buildAlignment(object direct, object reverse):
|
|
|
|
if len(direct)==0 or len(reverse)==0:
|
|
return None
|
|
|
|
la.seqA = direct
|
|
la.seqB = reverse
|
|
|
|
ali=la()
|
|
ali.direction='left'
|
|
|
|
ra.seqA = direct
|
|
ra.seqB = reverse
|
|
|
|
rali=ra()
|
|
rali.direction='right'
|
|
|
|
if ali.score < rali.score:
|
|
ali = rali
|
|
|
|
return ali
|
|
|
|
|
|
def alignmentIterator(entries, aligner):
|
|
|
|
if type(entries) == list:
|
|
two_views = True
|
|
forward = entries[0]
|
|
reverse = entries[1]
|
|
entries_len = len(forward)
|
|
else:
|
|
two_views = False
|
|
entries_len = len(entries)
|
|
|
|
for i in range(entries_len):
|
|
|
|
if two_views:
|
|
seqF = forward[i]
|
|
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.index = i
|
|
|
|
ali = aligner(seqF, seqR)
|
|
|
|
if ali is None:
|
|
continue
|
|
|
|
yield ali
|
|
|
|
|
|
def run(config):
|
|
|
|
DMS.obi_atexit()
|
|
|
|
logger("info", "obi alignpairedend")
|
|
|
|
# Open the input
|
|
|
|
two_views = False
|
|
forward = None
|
|
reverse = None
|
|
input = None
|
|
|
|
input = open_uri(config['obi']['inputURI'])
|
|
if input is None:
|
|
raise Exception("Could not open input reads")
|
|
if input[2] != View_NUC_SEQS:
|
|
raise NotImplementedError('obi alignpairedend only works on NUC_SEQS views')
|
|
|
|
if "reverse" in config["alignpairedend"]:
|
|
|
|
two_views = True
|
|
|
|
forward = input[1]
|
|
|
|
rinput = open_uri(config["alignpairedend"]["reverse"])
|
|
if rinput is None:
|
|
raise Exception("Could not open reverse reads")
|
|
if rinput[2] != View_NUC_SEQS:
|
|
raise NotImplementedError('obi alignpairedend only works on NUC_SEQS views')
|
|
|
|
reverse = rinput[1]
|
|
|
|
if len(forward) != len(reverse):
|
|
raise Exception("Error: the number of forward and reverse reads are different")
|
|
|
|
entries = [forward, reverse]
|
|
input_dms_name = [forward.dms.name, reverse.dms.name]
|
|
input_view_name = [forward.name, reverse.name]
|
|
|
|
else:
|
|
entries = input[1]
|
|
input_dms_name = [entries.dms.name]
|
|
input_view_name = [entries.name]
|
|
|
|
if two_views:
|
|
entries_len = len(forward)
|
|
else:
|
|
entries_len = len(entries)
|
|
|
|
# Open the output
|
|
output = open_uri(config['obi']['outputURI'],
|
|
input=False,
|
|
newviewtype=View_NUC_SEQS)
|
|
if output is None:
|
|
raise Exception("Could not create output view")
|
|
|
|
view = output[1]
|
|
|
|
Column.new_column(view, QUALITY_COLUMN, OBI_QUAL) #TODO output URI quality option?
|
|
|
|
if 'smin' in config['alignpairedend']:
|
|
smin = config['alignpairedend']['smin']
|
|
else:
|
|
smin = 0
|
|
|
|
# Initialize the progress bar
|
|
pb = ProgressBar(entries_len, config, seconde=5)
|
|
|
|
#if config['alignpairedend']['trueali']:
|
|
# kmer_ali = False
|
|
# aligner = buildAlignment
|
|
#else :
|
|
kmer_ali = True
|
|
if type(entries) == list:
|
|
forward = entries[0]
|
|
reverse = entries[1]
|
|
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'], \
|
|
reversed_column=entries[b'reversed']) # column created by the ngsfilter tool
|
|
|
|
ba = alignmentIterator(entries, aligner)
|
|
|
|
i = 0
|
|
for ali in ba:
|
|
|
|
pb(i)
|
|
|
|
PyErr_CheckSignals()
|
|
|
|
consensus = view[i]
|
|
|
|
if not two_views:
|
|
seqF = entries[i]
|
|
else:
|
|
seqF = forward[i]
|
|
|
|
if ali.score > smin and ali.consensus_len > 0 :
|
|
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])
|
|
else:
|
|
seqR = reverse[i]
|
|
buildJoinedSequence(ali, seqR, consensus, forward=seqF)
|
|
|
|
consensus[b"smin"] = smin
|
|
|
|
if kmer_ali :
|
|
ali.free()
|
|
|
|
i+=1
|
|
|
|
pb(i, force=True)
|
|
print("", file=sys.stderr)
|
|
|
|
if kmer_ali :
|
|
aligner.free()
|
|
|
|
# Save command config in View and DMS comments
|
|
command_line = " ".join(sys.argv[1:])
|
|
view.write_config(config, "alignpairedend", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
|
|
output[0].record_command_line(command_line)
|
|
|
|
#print("\n\nOutput view:\n````````````", file=sys.stderr)
|
|
#print(repr(view), file=sys.stderr)
|
|
|
|
input[0].close()
|
|
if two_views:
|
|
rinput[0].close()
|
|
output[0].close()
|
|
|
|
logger("info", "Done.")
|
|
|