def assignSequences(sets, fileInfo):
assert fileInfo.input_format in ('fq', 'fa')
if fileInfo.input_format == 'fq':
getID, getSeqs, nlines, outfmt = KTIO.getFastqIdentifier, KTIO.readFastq, 4, '%s\n%s\n+\n%s\n'
else:
getID, getSeqs, nlines, outfmt = KTIO.getFastaIdentifier, KTIO.readFasta, 2, '%s\n%s\n'
if fileInfo.gz_output:
ffmt = 'gz'
elif fileInfo.bz2_output:
ffmt = 'bz2'
else:
ffmt = None
R1gen, R2gen = getSeqs(fileInfo.inR1), None
R1A, R1B, R1AB, R1U = map(lambda x:KTIO.openFile(x, fmt=ffmt, mode='wb'), [fileInfo.outAR1, fileInfo.outBR1, fileInfo.outABR1, fileInfo.outUR1])
R2A, R2B, R2AB, R2U = None, None, None, None
if fileInfo.inR2 is not None:
R2gen = getSeqs(fileInfo.inR2)
R2A, R2B, R2AB, R2U = map(lambda x:KTIO.openFile(x, fmt=ffmt, mode='wb'), [fileInfo.outAR2, fileInfo.outBR2, fileInfo.outABR2, fileInfo.outUR2])
fxid1, fxid2 = None, None
while 1:
try:
R1rec = R1gen.next()
except:
break
fxid1, fxid2 = getID(R1rec[0]), None
if R2gen is not None:
try:
R2rec = R2gen.next()
except:
break
fxid2 = getID(R2rec[0])
assert fxid1 == fxid2 or fxid2 is None
# set order is A, B, AB
if fxid1 in sets[0]:
dest, destid = (R1A, R2A), 'A'
elif fxid1 in sets[1]:
dest, destid = (R1B, R2B), 'B'
elif fxid1 in sets[2]:
dest, destid = (R1AB, R2AB), '+'
else:
dest, destid = (R1U, R2U), 'U'
sys.stdout.write('\t'.join([destid, fxid1]) + '\n')
dest[0].write(outfmt % R1rec)
if dest[1] is not None:
dest[1].write(outfmt % R2rec)
map(lambda x:x.close(), [R1A, R1B, R1AB, R1U])
if R2A is not None:
map(lambda x:x.close(), [R2A, R2B, R2AB, R2U])
pass
def extractSequences_obsolete(keepSequences, fileInfo):
assert fileInfo.input_format in ('fq', 'fa')
if fileInfo.input_format == 'fq':
getID, getSeqs, nlines = KTIO.getFastqIdentifier, KTIO.readFastq, 4
else:
getID, getSeqs, nlines = KTIO.getFastaIdentifier, KTIO.readFasta, 2
if fileInfo.gz_output:
ffmt = 'gz'
elif fileInfo.bz2_output:
ffmt = 'bz2'
else:
ffmt = None
fwdOut, fwdGen = KTIO.openFile(fileInfo.outR1, mode='wb', fmt=ffmt), getSeqs(fileInfo.inR1)
revOut, revGen = None, None
if args.outR2 is not None and args.inR2 is not None:
revOut, revGen = KTIO.openFile(args.outR2, mode='wb', fmt=ffmt), getSeqs(args.inR2)
fxid1, fxid2 = None, None
while 1:
try:
fwdRecord = fwdGen.next()
except:
break
fxid1 = getID(fwdRecord[0])
if revGen is not None:
try:
revRecord = revGen.next()
except:
break
fxid2 = getID(revRecord[0])
assert fxid1 == fxid2 or fxid2 is None
if fxid1 in keepSequences:
fwdOut.write(('%s\n' * nlines) % fwdRecord)
if revOut is not None:
revOut.write(('%s\n' * nlines) % revRecord)
else:
pass
fwdOut.close()
if revOut is not None:
revOut.close()
pass
def filterSequences(db, f_inputClassification, keepTaxIDs, allowUnclassified=False, logfile=None):
if logfile is not None:
[logfile.write('Filtering sequences...\n'), logfile.flush()]
assert keepTaxIDs or allowUnclassified
nseqs = 0
keepSequences = set()
# need to keep track of all dropped sequences in case we want unclassified but used the --only-classified-output switch
# when running kraken (unclassified sequences are unmarked and need to be distinguished from unwanted sequences.)
dropSequences = set()
with KTIO.openFile(f_inputClassification) as fi:
for line in fi:
nseqs += 1
line = line.strip().split()
"""
if taxID > 0:
# extract reads from branch
# don't allow unclassified reads
takeUnclassified = allowUnclassified and line[0] == 'U'
# only allow reads that have been assigned a taxonomy id belonging to the branch
takeClassified = line[0] == 'C' and int(line[2]) in keepTaxIDs
elif taxID < 0:
# ignore reads from branch
# do not allow unclassified reads
takeUnclassified = allowUnclassified and line[0] == 'U'
# allow only reads that have been assigned a taxonomy id outside of the branch
takeClassified = line[0] == 'C' and int(line[2]) not in keepTaxIDs
else:
# extract unclassified
# allow unclassified reads
takeUnclassified = allowUnclassified and line[0] == 'U'
# don't allow classified reads
takeClassified = False
"""
takeClassified = line[0] == 'C' and int(line[2]) in keepTaxIDs
takeUnclassified = allowUnclassified and line[0] == 'U'
if takeUnclassified or takeClassified:
keepSequences.add(line[1].strip())
elif allowUnclassified:
# we want unclassified, but current line was classified and rejected
dropSequences.add(line[1].strip())
if logfile is not None:
logfile.write('Keeping %i of %i sequences (%.1f).\n' % (len(keepSequences), nseqs, float(len(keepSequences))/nseqs))
logfile.write('Dropping %i of %i sequences (%.1f).\n' % (len(dropSequences), nseqs, float(len(dropSequences))/nseqs))
logfile.flush()
return keepSequences, dropSequences
import sys
import csv
from ktoolu_io import readFastq, openFile
# call with samtools view -f2 or on bamfile with only -f2-mapping reads
#mappedReads = se()
#for row in csv.reader(sys.stdin, delimiter='\t'):
# mappedReads.add(row[0])
mappedReads = set(line.strip().split('\t')[0] for line in sys.stdin)
fq1 = readFastq(sys.argv[1])
fq2 = readFastq(sys.argv[2])
with openFile(sys.argv[1].replace('.fq.gz', '.unmapped_iwgsc10.fq.gz'),
fmt='gz',
mode='wt') as fo1, openFile(sys.argv[2].replace(
'.fq.gz', '.unmapped_iwgsc10.fq.gz'),
fmt='gz',
mode='wt') as fo2:
while 1:
try:
_id1, _seq1, _qual1 = next(fq1)
except:
break
_id2, _seq2, _qual2 = next(fq2)
if _id1[1:] not in mappedReads and _id2[1:] not in mappedReads:
fo1.write('{}\n{}\n+\n{}\n'.format(_id1, _seq1, _qual1))
fo2.write('{}\n{}\n+\n{}\n'.format(_id2, _seq2, _qual2))
def readClassification(fn):
with KTIO.openFile(fn) as fi:
return set(line.strip().split()[:2] for line in fi if line.strip().startswith('C'))
