def parse(fileName, junctions):
with open(fileName) as f:
for alnObj in psl_parser.read(f, 'track'):
tStarts = alnObj.attrib['tStarts']
blockSizes = alnObj.attrib['blockSizes']
tName = alnObj.attrib['tName']
construct(tName, tStarts, blockSizes, junctions)
def main(options, args):
exons = {}
clusters = {}
newClusterID = 0
clusterConnections = {}
linkedExons = {}
exonPositions = {}
endExons = {}
singleton = 0
print >> sys.stderr, 'Minimum UTR length = ', options.minimumUTRLength
print >> sys.stderr, 'Parsing and clustering exons..'
for n, alnObj in enumerate(psl_parser.read(open(options.infile), 'track')):
tStarts = alnObj.attrib['tStarts']
blockSizes = alnObj.attrib['blockSizes']
if len(blockSizes) == 1:
singleton += 1
tName = alnObj.attrib['tName']
newClusterID = construct(tName, tStarts, blockSizes, exons, clusters,
newClusterID, clusterConnections, linkedExons,
exonPositions, endExons)
if n % 1000 == 0:
print >> sys.stderr, '...', n
print >> sys.stderr, 'Total singletons = ', singleton
sumExons = {}
for ref, end in exons:
try:
sumExons[ref] += 1
except KeyError:
sumExons[ref] = 1
for ref in sorted(sumExons):
print >> sys.stderr, '\t%s has %d exon(s).' % (ref, sumExons[ref])
print >> sys.stderr, '\nTotal %d cluster(s) found.' % len(clusters)
print >> sys.stderr, '\nMerging clusters..'
mergedClusters = mergeClusters(clusters, clusterConnections)
print >> sys.stderr, '\nCleaning up..'
ignored = set([])
for cl in mergedClusters:
allExons = mergedClusters[cl]
cleanUpLinkedExons(allExons, linkedExons, exonPositions, ignored,
options.minimumUTRLength)
print >> sys.stderr, 'Modifying the right end of each transcript..'
for cl in mergedClusters:
findLongestEnd(mergedClusters[cl], linkedExons, endExons,
exonPositions, ignored)
print >> sys.stderr, '\nConstructing transcripts..'
allPaths = {}
visited = set([])
for n, cl in enumerate(mergedClusters):
txExons = sorted(mergedClusters[cl])
paths = buildPaths(linkedExons, txExons, allPaths, ignored, visited)
allPaths[cl] = paths
if n % 1000 == 0:
if n > 0:
print >> sys.stderr, '... %d built..' % n
genome = seqdb.SequenceFileDB(options.genome, verbose=False)
'''Create isoform objects from allPaths and
search for ORF.
'''
print >> sys.stderr, '\nBuilding gene models..'
allGenes = {}
n = 0
for chrom, geneID in allPaths:
n += 1
isoformID = 0
for isoExons in allPaths[(chrom, geneID)]:
isoform = Isoform(chrom, geneID, isoformID, isoExons, genome)
if chrom not in allGenes:
allGenes[chrom] = {}
allGenes[chrom][geneID] = [isoform]
else:
try:
allGenes[chrom][geneID].append(isoform)
except KeyError:
allGenes[chrom][geneID] = [isoform]
isoformID += 1
if n % 1000 == 0:
print >> sys.stderr, '...', n
print >> sys.stderr, '\nRemoving redundant sequences..'
findRedundantSequence(allGenes)
'''Creating sequence records for each DNA, RNA and protein sequences.'''
isoformDNASeqs = []
isoformProteinSeqs = []
isoformRNASeqs = []
totalGenes = 0
for chrom in allGenes:
for geneID in allGenes[chrom]:
totalGenes += 1
isoformID = 0
for isoform in allGenes[chrom][geneID]:
if not isoform.redundant:
isoform.isoformID = isoformID
isoformName = '%s:%d.%d' % (chrom, geneID,
isoform.isoformID)
DNARecord = SeqRecord(isoform.dnaSeq, id=isoformName)
isoformDNASeqs.append(DNARecord)
'''Search for ORF for non-redundant sequences'''
print >> sys.stderr, 'searching ORF: %s:%d.%d' \
% (chrom, geneID,isoformID)
findORF(isoform)
if isoform.frame:
proteinRecord = SeqRecord(isoform.proteinSeq,
id=isoformName)
RNARecord = SeqRecord(isoform.mrnaSeq, id=isoformName)
isoformProteinSeqs.append(proteinRecord)
isoformRNASeqs.append(RNARecord)
isoformID += 1
if n > 0 and n % 1000 == 0:
print >> sys.stderr, '...', n, 'transcripts done.'
print >> sys.stderr, 'Total genes = %d\n\n', totalGenes
print >> sys.stderr, 'Writing gene models to file...'
writeBEDFile(allGenes, options.basename)
print >> sys.stderr, 'Writing DNA sequences to file...'
SeqIO.write(isoformDNASeqs, options.basename + '.dnas.fa', 'fasta')
print >> sys.stderr, 'Writing RNA sequences to file...'
SeqIO.write(isoformRNASeqs, options.basename + '.mrnas.fa', 'fasta')
print >> sys.stderr, 'Writing protein sequences to file...'
SeqIO.write(isoformProteinSeqs, options.basename + '.proteins.fa', 'fasta')
def main(options, args):
exons = {}
clusters = {}
newClusterID = 0
clusterConnections = {}
linkedExons = {}
exonPositions = {}
endExons = {}
singleton = 0
print >> sys.stderr, 'Minimum UTR length = ', options.minimumUTRLength
print >> sys.stderr, 'Parsing and clustering exons..'
for n, alnObj in enumerate(psl_parser.read(open(options.infile), 'track')):
tStarts = alnObj.attrib['tStarts']
blockSizes = alnObj.attrib['blockSizes']
if len(blockSizes) == 1:
singleton += 1
tName = alnObj.attrib['tName']
newClusterID = construct(tName, tStarts, blockSizes,
exons, clusters, newClusterID,
clusterConnections,
linkedExons, exonPositions,
endExons)
if n % 1000 == 0:
print >> sys.stderr, '...', n
print >> sys.stderr, 'Total singletons = ', singleton
sumExons = {}
for ref, end in exons:
try:
sumExons[ref] += 1
except KeyError:
sumExons[ref] = 1
for ref in sorted(sumExons):
print >> sys.stderr, '\t%s has %d exon(s).' % (ref, sumExons[ref])
print >> sys.stderr, '\nTotal %d cluster(s) found.' % len(clusters)
print >> sys.stderr, '\nMerging clusters..'
mergedClusters = mergeClusters(clusters, clusterConnections)
print >> sys.stderr, '\nCleaning up..'
ignored = set([])
for cl in mergedClusters:
allExons = mergedClusters[cl]
cleanUpLinkedExons(allExons,
linkedExons,
exonPositions,
ignored,
options.minimumUTRLength)
print >> sys.stderr, 'Modifying the right end of each transcript..'
for cl in mergedClusters:
findLongestEnd(mergedClusters[cl],
linkedExons,
endExons,
exonPositions,
ignored)
print >> sys.stderr, '\nConstructing transcripts..'
allPaths = {}
visited = set([])
for n, cl in enumerate(mergedClusters):
txExons = sorted(mergedClusters[cl])
paths = buildPaths(linkedExons, txExons, allPaths, ignored, visited)
allPaths[cl] = paths
if n % 1000 == 0:
if n > 0:
print >> sys.stderr, '... %d built..' % n
genome = seqdb.SequenceFileDB(options.genome, verbose=False)
'''Create isoform objects from allPaths and
search for ORF.
'''
print >> sys.stderr, '\nBuilding gene models..'
allGenes = {}
n = 0
for chrom, geneID in allPaths:
n += 1
isoformID = 0
for isoExons in allPaths[(chrom, geneID)]:
isoform = Isoform(chrom, geneID, isoformID, isoExons, genome)
if chrom not in allGenes:
allGenes[chrom] = {}
allGenes[chrom][geneID] = [isoform]
else:
try:
allGenes[chrom][geneID].append(isoform)
except KeyError:
allGenes[chrom][geneID] = [isoform]
isoformID += 1
if n % 1000 == 0:
print >> sys.stderr, '...', n
print >> sys.stderr, '\nRemoving redundant sequences..'
findRedundantSequence(allGenes)
'''Creating sequence records for each DNA, RNA and protein sequences.'''
isoformDNASeqs = []
isoformProteinSeqs = []
isoformRNASeqs = []
totalGenes = 0
for chrom in allGenes:
for geneID in allGenes[chrom]:
totalGenes += 1
isoformID = 0
for isoform in allGenes[chrom][geneID]:
if not isoform.redundant:
isoform.isoformID = isoformID
isoformName = '%s:%d.%d' % (chrom,
geneID,
isoform.isoformID)
DNARecord = SeqRecord(isoform.dnaSeq,
id=isoformName)
isoformDNASeqs.append(DNARecord)
'''Search for ORF for non-redundant sequences'''
print >> sys.stderr, 'searching ORF: %s:%d.%d' \
% (chrom, geneID,isoformID)
findORF(isoform)
if isoform.frame:
proteinRecord = SeqRecord(isoform.proteinSeq,
id=isoformName)
RNARecord = SeqRecord(isoform.mrnaSeq,
id=isoformName)
isoformProteinSeqs.append(proteinRecord)
isoformRNASeqs.append(RNARecord)
isoformID += 1
if n > 0 and n % 1000 == 0:
print >> sys.stderr, '...', n, 'transcripts done.'
print >> sys.stderr, 'Total genes = %d\n\n', totalGenes
print >> sys.stderr, 'Writing gene models to file...'
writeBEDFile(allGenes, options.basename)
print >> sys.stderr, 'Writing DNA sequences to file...'
SeqIO.write(isoformDNASeqs, options.basename + '.dnas.fa', 'fasta')
print >> sys.stderr, 'Writing RNA sequences to file...'
SeqIO.write(isoformRNASeqs, options.basename + '.mrnas.fa', 'fasta')
print >> sys.stderr, 'Writing protein sequences to file...'
SeqIO.write(isoformProteinSeqs, options.basename + '.proteins.fa', 'fasta')
if exon_end == intron_start:
as_exons = [exon_start]
coverage = len([alread for alread in samfile.fetch(chr, exon_start, exon_end)])
print '>%d\t%d\t%d' % (exon_start, exon_end, coverage)
break
for intron_end in junctions[chr][intron_start]: # es = intron end site
ex_start = intron_end # intron end site = exon start site
for ex_end in exons[chr][ex_start]:
coverage = len([alread for alread in samfile.fetch(chr, ex_start , ex_end)])
print '%d\t%d\t%d' % (ex_start, ex_end, coverage)
as_exons.append(ex_end)
as_exons.sort()
print '%d-%d' % (as_exons[0], as_exons[-1])
if __name__ == '__main__':
fname = sys.argv[1]
samfile = pysam.Samfile(sys.argv[2], 'rb')
SNP_file = sys.argv[3]
comment = 'track'
all_transcripts = []
for line in psl_parser.read(open(fname), comment):
all_transcripts.append(line)
exons, junctions = construct(all_transcripts)
#AS_coverage(exons, junctions, samfile)
#cassette_exon(exons, junctions, samfile)
export_junctions(junctions)
