def isIndexRevComp(indexfile,indexes,n=500000):
"""Determine if the indexes are reverse complemented or not
:param indexfile: filename of the Fastq index file
:param indexes: list or tuple of index strings
:param n: integer number of reads to sample
"""
print("HERE")
ifile = Fastq(indexfile)
ilength=len(indexes[0])
print(ilength)
indexreads = collections.defaultdict(int)
for i in range(n):
indexreads[ifile.next().sequence[:ilength]]+=1
counts = {'normal':0,
'revcomp':0}
for k,v in list(indexreads.items()):
print(k,v)
for i in indexes:
if(pylev.levenshtein(k,i)<=1):
counts['normal']+=v
continue
if(pylev.levenshtein(k,revcomp(i))<=1):
counts['revcomp']+=v
if(counts['revcomp']>counts['normal']):
print('using revcomp')
else:
print('NOT revcomp')
return(counts['revcomp']>counts['normal'])
def isIndexRevComp(indexfile, indexes, n=500000):
"""Determine if the indexes are reverse complemented or not
:param indexfile: filename of the Fastq index file
:param indexes: list or tuple of index strings
:param n: integer number of reads to sample
"""
print("HERE")
ifile = Fastq(indexfile)
ilength = len(indexes[0])
print(ilength)
indexreads = collections.defaultdict(int)
for i in range(n):
indexreads[ifile.next().sequence[:ilength]] += 1
counts = {'normal': 0, 'revcomp': 0}
for k, v in list(indexreads.items()):
print(k, v)
for i in indexes:
if (pylev.levenshtein(k, i) <= 1):
counts['normal'] += v
continue
if (pylev.levenshtein(k, revcomp(i)) <= 1):
counts['revcomp'] += v
if (counts['revcomp'] > counts['normal']):
print('using revcomp')
else:
print('NOT revcomp')
return (counts['revcomp'] > counts['normal'])
def demultiplex(readfile,
indexfile,
indexes,
readfile2=None,
indexfile2=None):
"""Demultiplex from separate FASTQ files.
All FASTQ files can be gzipped (with suffix .gz).
:param readfile: The filename of the first fastq file
:param indexfile: The filename of the first index fastq file
:param indexes: An iterable of indexes. If dual-barcoding is used, the indexes should be comma-separated strings, one string for each barcode pair.
:param indexfile2: The filename of the second index fastq file. If this parameter is included, then the indexes parameter should be a set of comma-separated pairs of indexes.
:param readfile2: The filename of the second fastq file [optional]
"""
# single readfile, single indexfile
if(readfile2 is None) and (indexfile2 is None):
rfile1 = Fastq(readfile)
(rpath,rname) = os.path.split(readfile)
ifile = Fastq(indexfile)
indexRevComp = isIndexRevComp(indexfile,indexes)
existingIndexes = []
for i in indexes:
ofname1 = os.path.join(rpath,i + "_" + rname)
if(not os.path.exists(ofname1)):
ofile1[i]=fileOpen(os.path.join(rpath,i + "_" + rname),'w')
else:
print(ofname1," already exists, skipping")
existingIndexes.append(i)
for i in existingIndexes:
indexes.remove(i)
if(len(indexes)==0):
exit(0)
for (r1,i) in zip(rfile1,ifile):
try:
if indexRevComp:
i2 = revcomp(i.sequence[:indexlen])
ofile1[i2].write(str(r1))
else:
i2 = i.sequence[:indexlen]
ofile1[i2].write(str(r1))
except KeyError:
pass
rfile1.close()
ifile.close()
for ofile in list(ofile1.values()):
ofile.close()
## for i in indexes:
## os.rename(os.path.join(rpath,'tmp.' + i + "_" + rname),
## os.path.join(rpath,i + "_" + rname))
# two readfiles, single indexfile
if(readfile2 is not None) and (indexfile2 is None):
print("here1")
rfile1 = Fastq(readfile)
rfile2 = Fastq(readfile2)
(rpath,rname) = os.path.split(readfile)
(rpath2,rname2) = os.path.split(readfile2)
ifile = Fastq(indexfile)
indexRevComp = isIndexRevComp(indexfile,indexes)
ofile1 = {}
ofile2 = {}
existingIndexes = []
for i in indexes:
ofname1 = os.path.join(rpath,i + "_" + rname)
ofname2 = os.path.join(rpath2,i + "_" + rname2)
if(os.path.exists(ofname1) and os.path.exists(ofname2)):
print(ofname1,ofname2, " already exist, skipping")
existingIndexes.append(i)
else:
ofile1[i]=fileOpen(os.path.join(rpath,i + "_" + rname),'w')
ofile2[i]=fileOpen(os.path.join(rpath2,i + "_" + rname2),'w')
for i in existingIndexes:
indexes.remove(i)
if(len(indexes)==0):
exit(0)
indexlen = len(indexes[0])
for (r1,r2,i) in zip(rfile1,rfile2,ifile):
try:
if indexRevComp:
i2 = revcomp(i.sequence[:indexlen])
ofile1[i2].write(str(r1))
ofile2[i2].write(str(r2))
else:
i2 = i.sequence[:indexlen]
ofile1[i2].write(str(r1))
ofile2[i2].write(str(r2))
except KeyError:
pass
rfile1.close()
rfile2.close()
ifile.close()
for ofile in list(ofile1.values()):
ofile.close()
for ofile in list(ofile2.values()):
ofile.close()
## for i in indexes:
## print os.path.join(rpath,'tmp.' + i + "_" + rname),os.path.join(rpath,i + "_"+rname)
## os.rename(os.path.join(rpath,'tmp.' + i + "_" + rname),
## os.path.join(rpath,i + "_"+rname))
## os.rename(os.path.join(rpath2,'tmp.' + i +"_"+ rname2),
## os.path.join(rpath2,i +"_"+ rname2))
# two readfiles, two indexfiles
if(readfile2 is not None) and (indexfile2 is not None):
rfile1 = Fastq(readfile)
rfile2 = Fastq(readfile2)
(rpath,rname) = os.path.split(readfile)
(rpath2,rname2) = os.path.split(readfile2)
ifile = Fastq(indexfile)
ifile2 = Fastq(indexfile2)
indexes = [tuple(x.split(',')) for x in indexes]
indexRevComp = isIndexRevComp(indexfile,[i[0] for i in indexes])
ofile1 = {}
ofile2 = {}
existingIndexes = []
for j in indexes:
i = ''.join(j)
ofname1 = os.path.join(rpath,i + "_" + rname)
ofname2 = os.path.join(rpath2,i + "_" + rname2)
if(os.path.exists(ofname1) and os.path.exists(ofname2)):
print(ofname1,ofname2, " already exist, skipping")
existingIndexes.append(i)
else:
ofile1[i]=fileOpen(ofname1,'w')
ofile2[i]=fileOpen(ofname2,'w')
for i in existingIndexes:
indexes.remove(i)
if(len(indexes)==0):
exit(0)
indexlen = len(indexes[0][0])
for (r1,r2,i,i2) in zip(rfile1,rfile2,ifile,ifile2):
try:
if indexRevComp:
ir = revcomp(i.sequence[:indexlen])
ir2 = revcomp(i2.sequence[:indexlen])
istr = ir+ir2
ofile1[istr].write(str(r1))
ofile2[istr].write(str(r2))
else:
ir = i.sequence[:indexlen]
ir2 = i2.sequence[:indexlen]
istr = ir+ir2
ofile1[istr].write(str(r1))
ofile2[istr].write(str(r2))
except KeyError:
pass
rfile1.close()
rfile2.close()
ifile.close()
ifile2.close()
for ofile in list(ofile1.values()):
ofile.close()
for ofile in list(ofile2.values()):
ofile.close()
def demultiplex(readfile, indexfile, indexes, readfile2=None, indexfile2=None):
"""Demultiplex from separate FASTQ files.
All FASTQ files can be gzipped (with suffix .gz).
:param readfile: The filename of the first fastq file
:param indexfile: The filename of the first index fastq file
:param indexes: An iterable of indexes. If dual-barcoding is used, the indexes should be comma-separated strings, one string for each barcode pair.
:param indexfile2: The filename of the second index fastq file. If this parameter is included, then the indexes parameter should be a set of comma-separated pairs of indexes.
:param readfile2: The filename of the second fastq file [optional]
"""
# single readfile, single indexfile
if (readfile2 is None) and (indexfile2 is None):
rfile1 = Fastq(readfile)
(rpath, rname) = os.path.split(readfile)
ifile = Fastq(indexfile)
indexRevComp = isIndexRevComp(indexfile, indexes)
existingIndexes = []
for i in indexes:
ofname1 = os.path.join(rpath, i + "_" + rname)
if (not os.path.exists(ofname1)):
ofile1[i] = fileOpen(os.path.join(rpath, i + "_" + rname), 'w')
else:
print(ofname1, " already exists, skipping")
existingIndexes.append(i)
for i in existingIndexes:
indexes.remove(i)
if (len(indexes) == 0):
exit(0)
for (r1, i) in zip(rfile1, ifile):
try:
if indexRevComp:
i2 = revcomp(i.sequence[:indexlen])
ofile1[i2].write(str(r1))
else:
i2 = i.sequence[:indexlen]
ofile1[i2].write(str(r1))
except KeyError:
pass
rfile1.close()
ifile.close()
for ofile in list(ofile1.values()):
ofile.close()
## for i in indexes:
## os.rename(os.path.join(rpath,'tmp.' + i + "_" + rname),
## os.path.join(rpath,i + "_" + rname))
# two readfiles, single indexfile
if (readfile2 is not None) and (indexfile2 is None):
print("here1")
rfile1 = Fastq(readfile)
rfile2 = Fastq(readfile2)
(rpath, rname) = os.path.split(readfile)
(rpath2, rname2) = os.path.split(readfile2)
ifile = Fastq(indexfile)
indexRevComp = isIndexRevComp(indexfile, indexes)
ofile1 = {}
ofile2 = {}
existingIndexes = []
for i in indexes:
ofname1 = os.path.join(rpath, i + "_" + rname)
ofname2 = os.path.join(rpath2, i + "_" + rname2)
if (os.path.exists(ofname1) and os.path.exists(ofname2)):
print(ofname1, ofname2, " already exist, skipping")
existingIndexes.append(i)
else:
ofile1[i] = fileOpen(os.path.join(rpath, i + "_" + rname), 'w')
ofile2[i] = fileOpen(os.path.join(rpath2, i + "_" + rname2),
'w')
for i in existingIndexes:
indexes.remove(i)
if (len(indexes) == 0):
exit(0)
indexlen = len(indexes[0])
for (r1, r2, i) in zip(rfile1, rfile2, ifile):
try:
if indexRevComp:
i2 = revcomp(i.sequence[:indexlen])
ofile1[i2].write(str(r1))
ofile2[i2].write(str(r2))
else:
i2 = i.sequence[:indexlen]
ofile1[i2].write(str(r1))
ofile2[i2].write(str(r2))
except KeyError:
pass
rfile1.close()
rfile2.close()
ifile.close()
for ofile in list(ofile1.values()):
ofile.close()
for ofile in list(ofile2.values()):
ofile.close()
## for i in indexes:
## print os.path.join(rpath,'tmp.' + i + "_" + rname),os.path.join(rpath,i + "_"+rname)
## os.rename(os.path.join(rpath,'tmp.' + i + "_" + rname),
## os.path.join(rpath,i + "_"+rname))
## os.rename(os.path.join(rpath2,'tmp.' + i +"_"+ rname2),
## os.path.join(rpath2,i +"_"+ rname2))
# two readfiles, two indexfiles
if (readfile2 is not None) and (indexfile2 is not None):
rfile1 = Fastq(readfile)
rfile2 = Fastq(readfile2)
(rpath, rname) = os.path.split(readfile)
(rpath2, rname2) = os.path.split(readfile2)
ifile = Fastq(indexfile)
ifile2 = Fastq(indexfile2)
indexes = [tuple(x.split(',')) for x in indexes]
indexRevComp = isIndexRevComp(indexfile, [i[0] for i in indexes])
ofile1 = {}
ofile2 = {}
existingIndexes = []
for j in indexes:
i = ''.join(j)
ofname1 = os.path.join(rpath, i + "_" + rname)
ofname2 = os.path.join(rpath2, i + "_" + rname2)
if (os.path.exists(ofname1) and os.path.exists(ofname2)):
print(ofname1, ofname2, " already exist, skipping")
existingIndexes.append(i)
else:
ofile1[i] = fileOpen(ofname1, 'w')
ofile2[i] = fileOpen(ofname2, 'w')
for i in existingIndexes:
indexes.remove(i)
if (len(indexes) == 0):
exit(0)
indexlen = len(indexes[0][0])
for (r1, r2, i, i2) in zip(rfile1, rfile2, ifile, ifile2):
try:
if indexRevComp:
ir = revcomp(i.sequence[:indexlen])
ir2 = revcomp(i2.sequence[:indexlen])
istr = ir + ir2
ofile1[istr].write(str(r1))
ofile2[istr].write(str(r2))
else:
ir = i.sequence[:indexlen]
ir2 = i2.sequence[:indexlen]
istr = ir + ir2
ofile1[istr].write(str(r1))
ofile2[istr].write(str(r2))
except KeyError:
pass
rfile1.close()
rfile2.close()
ifile.close()
ifile2.close()
for ofile in list(ofile1.values()):
ofile.close()
for ofile in list(ofile2.values()):
ofile.close()
