def makeTranscriptome(tranFN, outFN):
p = bioLibCG.cgPrint()
p.show = False
gf = GenomeFetch.GenomeFetch('hg19')
fOut = open(outFN, 'w')
f = open(tranFN, 'r')
for line in f:
ls = line.strip().split('\t')
tChrom, tStrand = ls[1], bioLibCG.switchStrandFormat(ls[2])
exonStarts = [int(x) + 1 for x in ls[8][:-1].split(',')]
exonEnds = [int(x) for x in ls[9][:-1].split(',')]
exonPairs = zip(exonStarts, exonEnds)
tID = ls[0]
gID = ls[10]
seqList = []
for eStart, eEnd in exonPairs:
tcc = bioLibCG.makeTcc(tChrom, tStrand, eStart, eEnd)
seqList.append(gf.getSequence(tcc))
mRNA = ''.join(seqList)
#reverse direction if negative strand
if tStrand == '-1':
mRNA = mRNA[::-1]
fOut.write('> %s:%s:%s\n' % (tID, gID, len(mRNA)))
fOut.write(mRNA + '\n\n')
fOut.close()
f.close()
def makeTranscriptome(tranFN, outFN):
p = bioLibCG.cgPrint()
p.show = False
gf = GenomeFetch.GenomeFetch('hg19')
fOut = open(outFN, 'w')
f = open(tranFN, 'r')
for line in f:
ls = line.strip().split('\t')
tChrom, tStrand = ls[1], bioLibCG.switchStrandFormat(ls[2])
exonStarts = [int(x) + 1 for x in ls[8][:-1].split(',')]
exonEnds = [int(x) for x in ls[9][:-1].split(',')]
exonPairs = zip(exonStarts, exonEnds)
tID = ls[0]
gID = ls[10]
seqList = []
for eStart, eEnd in exonPairs:
tcc = bioLibCG.makeTcc(tChrom, tStrand, eStart, eEnd)
seqList.append(gf.getSequence(tcc))
mRNA = ''.join(seqList)
#reverse direction if negative strand
if tStrand == '-1':
mRNA = mRNA[::-1]
fOut.write('> %s:%s:%s\n' % (tID, gID, len(mRNA)))
fOut.write(mRNA + '\n\n')
fOut.close()
f.close()
def checkMessy(tranFN):
p = bioLibCG.cgPrint()
f = open(tranFN, 'r')
a = 0
b = 0
c = 0
d = 0
e = 0
for line in f:
ls = line.strip().split('\t')
chrom, strand = ls[1], bioLibCG.switchStrandFormat(ls[2])
tStart, tEnd = int(ls[3]), int(ls[4]) - 1
cStart, cEnd = int(ls[5]), int(ls[6]) - 1
exonStarts = [int(x) for x in ls[8][:-1].split(',')]
exonEnds = [int(x) - 1 for x in ls[9][:-1].split(',')]
exonPairs = zip(exonStarts, exonEnds)
codingStatus = '_coding' in ls[15]
tID = ls[0]
#debug
p.show = False
intronPairs = []
i = 0
for pair in exonPairs:
if i == 0:
i += 1
continue
iStart = exonPairs[i -1][1] + 1
iEnd = exonPairs[i][0] - 1
intronPairs.append((iStart, iEnd))
i += 1
#p.tell(tStart, tEnd, cStart, cEnd, exonPairs, intronPairs)
#take care of messy UTRs and assign utr ranges
#5UTR
if strand == '1':
if cStart == tStart or cStart == tEnd + 1:
p.tell('5 is none')
b += 1
if codingStatus:
d += 1
range5 = ()
else:
range5 = (tStart, cStart - 1)
else:
if cEnd + 1 == tStart or cEnd + 1 == tEnd + 1:
p.tell('5 is none')
b += 1
if codingStatus:
d += 1
range5 = ()
else:
range5 = (cEnd + 1, tEnd)
#3UTR
if strand == '1':
if cEnd + 1 == tStart or cEnd + 1 == tEnd + 1:
p.tell('3 is none')
c += 1
if codingStatus:
e += 1
range3 = ()
else:
range3 = (cEnd + 1, tEnd)
else:
if cStart == tStart or cStart == tEnd + 1:
p.tell('3 is none')
c += 1
if codingStatus:
e += 1
range3 = ()
else:
range3 = (tStart, cStart - 1)
a += 1
print a, b, c, d, e
def checkMessy(tranFN):
p = bioLibCG.cgPrint()
f = open(tranFN, 'r')
a = 0
b = 0
c = 0
d = 0
e = 0
for line in f:
ls = line.strip().split('\t')
chrom, strand = ls[1], bioLibCG.switchStrandFormat(ls[2])
tStart, tEnd = int(ls[3]), int(ls[4]) - 1
cStart, cEnd = int(ls[5]), int(ls[6]) - 1
exonStarts = [int(x) for x in ls[8][:-1].split(',')]
exonEnds = [int(x) - 1 for x in ls[9][:-1].split(',')]
exonPairs = zip(exonStarts, exonEnds)
codingStatus = '_coding' in ls[15]
tID = ls[0]
#debug
p.show = False
intronPairs = []
i = 0
for pair in exonPairs:
if i == 0:
i += 1
continue
iStart = exonPairs[i - 1][1] + 1
iEnd = exonPairs[i][0] - 1
intronPairs.append((iStart, iEnd))
i += 1
#p.tell(tStart, tEnd, cStart, cEnd, exonPairs, intronPairs)
#take care of messy UTRs and assign utr ranges
#5UTR
if strand == '1':
if cStart == tStart or cStart == tEnd + 1:
p.tell('5 is none')
b += 1
if codingStatus:
d += 1
range5 = ()
else:
range5 = (tStart, cStart - 1)
else:
if cEnd + 1 == tStart or cEnd + 1 == tEnd + 1:
p.tell('5 is none')
b += 1
if codingStatus:
d += 1
range5 = ()
else:
range5 = (cEnd + 1, tEnd)
#3UTR
if strand == '1':
if cEnd + 1 == tStart or cEnd + 1 == tEnd + 1:
p.tell('3 is none')
c += 1
if codingStatus:
e += 1
range3 = ()
else:
range3 = (cEnd + 1, tEnd)
else:
if cStart == tStart or cStart == tEnd + 1:
p.tell('3 is none')
c += 1
if codingStatus:
e += 1
range3 = ()
else:
range3 = (tStart, cStart - 1)
a += 1
print a, b, c, d, e
def makeContextWig(tranFN, wigDir, chrom, strand, species = 'hg19'):
p = bioLibCG.cgPrint()
coord_id = {}
f = open(tranFN, 'r')
for line in f:
ls = line.strip().split('\t')
tChrom, tStrand = ls[1], bioLibCG.switchStrandFormat(ls[2])
if tChrom != chrom or tStrand != strand:
continue
tStart, tEnd = int(ls[3]), int(ls[4]) - 1
cStart, cEnd = int(ls[5]), int(ls[6]) - 1
exonStarts = [int(x) for x in ls[8][:-1].split(',')]
exonEnds = [int(x) - 1 for x in ls[9][:-1].split(',')]
exonPairs = zip(exonStarts, exonEnds)
codingStatus = '_coding' in ls[13]
tID = ls[0]
#debug
p.show = False
intronPairs = []
i = 0
for pair in exonPairs:
if i == 0:
i += 1
continue
iStart = exonPairs[i -1][1] + 1
iEnd = exonPairs[i][0] - 1
intronPairs.append((iStart, iEnd))
i += 1
#p.tell(tStart, tEnd, cStart, cEnd, exonPairs, intronPairs)
#take care of messy UTRs and assign utr ranges
#5UTR
if strand == '1':
if cStart == tStart or cStart == tEnd + 1:
p.tell('5 is none')
range5 = ()
else:
range5 = (tStart, cStart - 1)
else:
if cEnd + 1 == tStart or cEnd + 1 == tEnd + 1:
p.tell('5 is none')
range5 = ()
else:
range5 = (cEnd + 1, tEnd)
#3UTR
if strand == '1':
if cEnd + 1 == tStart or cEnd + 1 == tEnd + 1:
p.tell('3 is none')
range3 = ()
else:
range3 = (cEnd + 1, tEnd)
else:
if cStart == tStart or cStart == tEnd + 1:
p.tell('3 is none')
range3 = ()
else:
range3 = (tStart, cStart - 1)
p.tell('ranges', range5, range3)
p.tell('intronRange', intronPairs)
utr5 = compareData.subtractTwoRanges([range5], intronPairs)
utr3 = compareData.subtractTwoRanges([range3], intronPairs)
p.tell('utr', utr5, utr3)
p.tell('exon before', exonPairs)
exonPairs = compareData.subtractTwoRanges(exonPairs, [range5])
exonPairs = compareData.subtractTwoRanges(exonPairs, [range3])
p.tell('exon after', exonPairs)
debugSpot = 23631989
#5UTR
for pair in utr5:
p.tell('filling utr5', pair[0], pair[1])
for i in xrange(pair[0], pair[1] + 1):
if i == debugSpot: p.tell('*** 5UTR', codingStatus, tID)
if codingStatus:
coord_id[i] = coord_id.get(i, '') + 'C_5UTR '
else:
coord_id[i] = coord_id.get(i, '') + 'NC_5UTR '
#Exons
for pair in exonPairs:
p.tell('filling exons', pair[0], pair[1])
for i in xrange(pair[0], pair[1] + 1):
if i == debugSpot: p.tell('*** exon', codingStatus, tID)
if codingStatus:
coord_id[i] = coord_id.get(i, '') + 'C_EXON '
else:
coord_id[i] = coord_id.get(i, '') + 'NC_EXON '
#Introns
for pair in intronPairs:
p.tell('filling introns', pair[0], pair[1])
for i in xrange(pair[0], pair[1] + 1):
if i == debugSpot: p.tell('*** INTRON', codingStatus, tID)
if codingStatus:
coord_id[i] = coord_id.get(i, '') + 'C_INTRON '
else:
coord_id[i] = coord_id.get(i, '') + 'NC_INTRON '
#3UTR
for pair in utr3:
p.tell('filling utr3', pair[0], pair[1])
for i in xrange(pair[0], pair[1] + 1):
if i == debugSpot: p.tell(' *** 3UTR', codingStatus, tID)
if codingStatus:
coord_id[i] = coord_id.get(i, '') + 'C_3UTR '
else:
coord_id[i] = coord_id.get(i, '') + 'NC_3UTR '
p.show = False
#uniqify, stringify
for i, ids in coord_id.iteritems():
coord_id[i] = ','.join([x for x in set(ids.strip().split(' '))])
#p.tell('finalInfo', utr5, exonPairs, utr3)
#write wig to file
writeWigDictToWig(coord_id, chrom, strand, species, 'context', wigDir, 'INTER')
def makeContextWig(tranFN, wigDir, chrom, strand, species='hg19'):
p = bioLibCG.cgPrint()
coord_id = {}
f = open(tranFN, 'r')
for line in f:
ls = line.strip().split('\t')
tChrom, tStrand = ls[1], bioLibCG.switchStrandFormat(ls[2])
if tChrom != chrom or tStrand != strand:
continue
tStart, tEnd = int(ls[3]), int(ls[4]) - 1
cStart, cEnd = int(ls[5]), int(ls[6]) - 1
exonStarts = [int(x) for x in ls[8][:-1].split(',')]
exonEnds = [int(x) - 1 for x in ls[9][:-1].split(',')]
exonPairs = zip(exonStarts, exonEnds)
codingStatus = '_coding' in ls[13]
tID = ls[0]
#debug
p.show = False
intronPairs = []
i = 0
for pair in exonPairs:
if i == 0:
i += 1
continue
iStart = exonPairs[i - 1][1] + 1
iEnd = exonPairs[i][0] - 1
intronPairs.append((iStart, iEnd))
i += 1
#p.tell(tStart, tEnd, cStart, cEnd, exonPairs, intronPairs)
#take care of messy UTRs and assign utr ranges
#5UTR
if strand == '1':
if cStart == tStart or cStart == tEnd + 1:
p.tell('5 is none')
range5 = ()
else:
range5 = (tStart, cStart - 1)
else:
if cEnd + 1 == tStart or cEnd + 1 == tEnd + 1:
p.tell('5 is none')
range5 = ()
else:
range5 = (cEnd + 1, tEnd)
#3UTR
if strand == '1':
if cEnd + 1 == tStart or cEnd + 1 == tEnd + 1:
p.tell('3 is none')
range3 = ()
else:
range3 = (cEnd + 1, tEnd)
else:
if cStart == tStart or cStart == tEnd + 1:
p.tell('3 is none')
range3 = ()
else:
range3 = (tStart, cStart - 1)
p.tell('ranges', range5, range3)
p.tell('intronRange', intronPairs)
utr5 = compareData.subtractTwoRanges([range5], intronPairs)
utr3 = compareData.subtractTwoRanges([range3], intronPairs)
p.tell('utr', utr5, utr3)
p.tell('exon before', exonPairs)
exonPairs = compareData.subtractTwoRanges(exonPairs, [range5])
exonPairs = compareData.subtractTwoRanges(exonPairs, [range3])
p.tell('exon after', exonPairs)
debugSpot = 23631989
#5UTR
for pair in utr5:
p.tell('filling utr5', pair[0], pair[1])
for i in xrange(pair[0], pair[1] + 1):
if i == debugSpot: p.tell('*** 5UTR', codingStatus, tID)
if codingStatus:
coord_id[i] = coord_id.get(i, '') + 'C_5UTR '
else:
coord_id[i] = coord_id.get(i, '') + 'NC_5UTR '
#Exons
for pair in exonPairs:
p.tell('filling exons', pair[0], pair[1])
for i in xrange(pair[0], pair[1] + 1):
if i == debugSpot: p.tell('*** exon', codingStatus, tID)
if codingStatus:
coord_id[i] = coord_id.get(i, '') + 'C_EXON '
else:
coord_id[i] = coord_id.get(i, '') + 'NC_EXON '
#Introns
for pair in intronPairs:
p.tell('filling introns', pair[0], pair[1])
for i in xrange(pair[0], pair[1] + 1):
if i == debugSpot: p.tell('*** INTRON', codingStatus, tID)
if codingStatus:
coord_id[i] = coord_id.get(i, '') + 'C_INTRON '
else:
coord_id[i] = coord_id.get(i, '') + 'NC_INTRON '
#3UTR
for pair in utr3:
p.tell('filling utr3', pair[0], pair[1])
for i in xrange(pair[0], pair[1] + 1):
if i == debugSpot: p.tell(' *** 3UTR', codingStatus, tID)
if codingStatus:
coord_id[i] = coord_id.get(i, '') + 'C_3UTR '
else:
coord_id[i] = coord_id.get(i, '') + 'NC_3UTR '
p.show = False
#uniqify, stringify
for i, ids in coord_id.iteritems():
coord_id[i] = ','.join([x for x in set(ids.strip().split(' '))])
#p.tell('finalInfo', utr5, exonPairs, utr3)
#write wig to file
writeWigDictToWig(coord_id, chrom, strand, species, 'context', wigDir,
'INTER')
