def process_gene_model(gene_model): print >>sys.stderr, "processing " + gene_model + ' ...', obj = BED.ParseBED(gene_model) utr_3 = obj.getUTR(utr=3) utr_5 = obj.getUTR(utr=5) cds_exon = obj.getCDSExon() intron = obj.getIntron() intron = BED.unionBed3(intron) cds_exon=BED.unionBed3(cds_exon) utr_5 = BED.unionBed3(utr_5) utr_3 = BED.unionBed3(utr_3) utr_5 = BED.subtractBed3(utr_5,cds_exon) utr_3 = BED.subtractBed3(utr_3,cds_exon) intron = BED.subtractBed3(intron,cds_exon) intron = BED.subtractBed3(intron,utr_5) intron = BED.subtractBed3(intron,utr_3) intergenic_up_1kb = obj.getIntergenic(direction="up",size=1000) intergenic_down_1kb = obj.getIntergenic(direction="down",size=1000) intergenic_up_5kb = obj.getIntergenic(direction="up",size=5000) intergenic_down_5kb = obj.getIntergenic(direction="down",size=5000) intergenic_up_10kb = obj.getIntergenic(direction="up",size=10000) intergenic_down_10kb = obj.getIntergenic(direction="down",size=10000) #merge integenic region intergenic_up_1kb=BED.unionBed3(intergenic_up_1kb) intergenic_up_5kb=BED.unionBed3(intergenic_up_5kb) intergenic_up_10kb=BED.unionBed3(intergenic_up_10kb) intergenic_down_1kb=BED.unionBed3(intergenic_down_1kb) intergenic_down_5kb=BED.unionBed3(intergenic_down_5kb) intergenic_down_10kb=BED.unionBed3(intergenic_down_10kb) #purify intergenic region intergenic_up_1kb=BED.subtractBed3(intergenic_up_1kb,cds_exon) intergenic_up_1kb=BED.subtractBed3(intergenic_up_1kb,utr_5) intergenic_up_1kb=BED.subtractBed3(intergenic_up_1kb,utr_3) intergenic_up_1kb=BED.subtractBed3(intergenic_up_1kb,intron) intergenic_down_1kb=BED.subtractBed3(intergenic_down_1kb,cds_exon) intergenic_down_1kb=BED.subtractBed3(intergenic_down_1kb,utr_5) intergenic_down_1kb=BED.subtractBed3(intergenic_down_1kb,utr_3) intergenic_down_1kb=BED.subtractBed3(intergenic_down_1kb,intron) #purify intergenic region intergenic_up_5kb=BED.subtractBed3(intergenic_up_5kb,cds_exon) intergenic_up_5kb=BED.subtractBed3(intergenic_up_5kb,utr_5) intergenic_up_5kb=BED.subtractBed3(intergenic_up_5kb,utr_3) intergenic_up_5kb=BED.subtractBed3(intergenic_up_5kb,intron) intergenic_down_5kb=BED.subtractBed3(intergenic_down_5kb,cds_exon) intergenic_down_5kb=BED.subtractBed3(intergenic_down_5kb,utr_5) intergenic_down_5kb=BED.subtractBed3(intergenic_down_5kb,utr_3) intergenic_down_5kb=BED.subtractBed3(intergenic_down_5kb,intron) #purify intergenic region intergenic_up_10kb=BED.subtractBed3(intergenic_up_10kb,cds_exon) intergenic_up_10kb=BED.subtractBed3(intergenic_up_10kb,utr_5) intergenic_up_10kb=BED.subtractBed3(intergenic_up_10kb,utr_3) intergenic_up_10kb=BED.subtractBed3(intergenic_up_10kb,intron) intergenic_down_10kb=BED.subtractBed3(intergenic_down_10kb,cds_exon) intergenic_down_10kb=BED.subtractBed3(intergenic_down_10kb,utr_5) intergenic_down_10kb=BED.subtractBed3(intergenic_down_10kb,utr_3) intergenic_down_10kb=BED.subtractBed3(intergenic_down_10kb,intron) #build intervalTree cds_exon_ranges = build_bitsets(cds_exon) utr_5_ranges = build_bitsets(utr_5) utr_3_ranges = build_bitsets(utr_3) intron_ranges = build_bitsets(intron) interg_ranges_up_1kb_ranges = build_bitsets(intergenic_up_1kb) interg_ranges_up_5kb_ranges = build_bitsets(intergenic_up_5kb) interg_ranges_up_10kb_ranges = build_bitsets(intergenic_up_10kb) interg_ranges_down_1kb_ranges = build_bitsets(intergenic_down_1kb) interg_ranges_down_5kb_ranges = build_bitsets(intergenic_down_5kb) interg_ranges_down_10kb_ranges = build_bitsets(intergenic_down_10kb) exon_size = cal_size(cds_exon) intron_size = cal_size(intron) utr3_size = cal_size(utr_3) utr5_size = cal_size(utr_5) int_up1k_size = cal_size(intergenic_up_1kb) int_up5k_size = cal_size(intergenic_up_5kb) int_up10k_size = cal_size(intergenic_up_10kb) int_down1k_size = cal_size(intergenic_down_1kb) int_down5k_size = cal_size(intergenic_down_5kb) int_down10k_size = cal_size(intergenic_down_10kb) print >>sys.stderr, "Done" return (cds_exon_ranges,intron_ranges,utr_5_ranges,utr_3_ranges,\ interg_ranges_up_1kb_ranges,interg_ranges_up_5kb_ranges,interg_ranges_up_10kb_ranges,\ interg_ranges_down_1kb_ranges,interg_ranges_down_5kb_ranges,interg_ranges_down_10kb_ranges,\ exon_size,intron_size,utr5_size,utr3_size,\ int_up1k_size,int_up5k_size,int_up10k_size,\ int_down1k_size,int_down5k_size,int_down10k_size)
def process_gene_model(gene_model): print >>sys.stderr, "processing " + gene_model + ' ...', obj = BED.ParseBED(gene_model) utr_3 = obj.getUTR(utr=3) utr_5 = obj.getUTR(utr=5) cds_exon = obj.getCDSExon() intron = obj.getIntron() intron = BED.unionBed3(intron) cds_exon=BED.unionBed3(cds_exon) utr_5 = BED.unionBed3(utr_5) utr_3 = BED.unionBed3(utr_3) utr_5 = BED.subtractBed3(utr_5,cds_exon) utr_3 = BED.subtractBed3(utr_3,cds_exon) intron = BED.subtractBed3(intron,cds_exon) intron = BED.subtractBed3(intron,utr_5) intron = BED.subtractBed3(intron,utr_3) intergenic_up_1kb = obj.getIntergenic(direction="up",size=1000) intergenic_down_1kb = obj.getIntergenic(direction="down",size=1000) intergenic_up_5kb = obj.getIntergenic(direction="up",size=5000) intergenic_down_5kb = obj.getIntergenic(direction="down",size=5000) intergenic_up_10kb = obj.getIntergenic(direction="up",size=10000) intergenic_down_10kb = obj.getIntergenic(direction="down",size=10000) #merge integenic region intergenic_up_1kb=BED.unionBed3(intergenic_up_1kb) intergenic_up_5kb=BED.unionBed3(intergenic_up_5kb) intergenic_up_10kb=BED.unionBed3(intergenic_up_10kb) intergenic_down_1kb=BED.unionBed3(intergenic_down_1kb) intergenic_down_5kb=BED.unionBed3(intergenic_down_5kb) intergenic_down_10kb=BED.unionBed3(intergenic_down_10kb) #purify intergenic region intergenic_up_1kb=BED.subtractBed3(intergenic_up_1kb,cds_exon) intergenic_up_1kb=BED.subtractBed3(intergenic_up_1kb,utr_5) intergenic_up_1kb=BED.subtractBed3(intergenic_up_1kb,utr_3) intergenic_up_1kb=BED.subtractBed3(intergenic_up_1kb,intron) intergenic_down_1kb=BED.subtractBed3(intergenic_down_1kb,cds_exon) intergenic_down_1kb=BED.subtractBed3(intergenic_down_1kb,utr_5) intergenic_down_1kb=BED.subtractBed3(intergenic_down_1kb,utr_3) intergenic_down_1kb=BED.subtractBed3(intergenic_down_1kb,intron) #purify intergenic region intergenic_up_5kb=BED.subtractBed3(intergenic_up_5kb,cds_exon) intergenic_up_5kb=BED.subtractBed3(intergenic_up_5kb,utr_5) intergenic_up_5kb=BED.subtractBed3(intergenic_up_5kb,utr_3) intergenic_up_5kb=BED.subtractBed3(intergenic_up_5kb,intron) intergenic_down_5kb=BED.subtractBed3(intergenic_down_5kb,cds_exon) intergenic_down_5kb=BED.subtractBed3(intergenic_down_5kb,utr_5) intergenic_down_5kb=BED.subtractBed3(intergenic_down_5kb,utr_3) intergenic_down_5kb=BED.subtractBed3(intergenic_down_5kb,intron) #purify intergenic region intergenic_up_10kb=BED.subtractBed3(intergenic_up_10kb,cds_exon) intergenic_up_10kb=BED.subtractBed3(intergenic_up_10kb,utr_5) intergenic_up_10kb=BED.subtractBed3(intergenic_up_10kb,utr_3) intergenic_up_10kb=BED.subtractBed3(intergenic_up_10kb,intron) intergenic_down_10kb=BED.subtractBed3(intergenic_down_10kb,cds_exon) intergenic_down_10kb=BED.subtractBed3(intergenic_down_10kb,utr_5) intergenic_down_10kb=BED.subtractBed3(intergenic_down_10kb,utr_3) intergenic_down_10kb=BED.subtractBed3(intergenic_down_10kb,intron) #build intervalTree cds_exon_ranges = build_bitsets(cds_exon) utr_5_ranges = build_bitsets(utr_5) utr_3_ranges = build_bitsets(utr_3) intron_ranges = build_bitsets(intron) interg_ranges_up_1kb_ranges = build_bitsets(intergenic_up_1kb) interg_ranges_up_5kb_ranges = build_bitsets(intergenic_up_5kb) interg_ranges_up_10kb_ranges = build_bitsets(intergenic_up_10kb) interg_ranges_down_1kb_ranges = build_bitsets(intergenic_down_1kb) interg_ranges_down_5kb_ranges = build_bitsets(intergenic_down_5kb) interg_ranges_down_10kb_ranges = build_bitsets(intergenic_down_10kb) exon_size = cal_size(cds_exon) intron_size = cal_size(intron) utr3_size = cal_size(utr_3) utr5_size = cal_size(utr_5) int_up1k_size = cal_size(intergenic_up_1kb) int_up5k_size = cal_size(intergenic_up_5kb) int_up10k_size = cal_size(intergenic_up_10kb) int_down1k_size = cal_size(intergenic_down_1kb) int_down5k_size = cal_size(intergenic_down_5kb) int_down10k_size = cal_size(intergenic_down_10kb) print >>sys.stderr, "Done" return (cds_exon_ranges,intron_ranges,utr_5_ranges,utr_3_ranges,\ interg_ranges_up_1kb_ranges,interg_ranges_up_5kb_ranges,interg_ranges_up_10kb_ranges,\ interg_ranges_down_1kb_ranges,interg_ranges_down_5kb_ranges,interg_ranges_down_10kb_ranges,\ exon_size,intron_size,utr5_size,utr3_size,\ int_up1k_size,int_up5k_size,int_up10k_size,\ int_down1k_size,int_down5k_size,int_down10k_size)
def main():
usage="%prog [options]" + '\n' + __doc__ + "\n"
parser = OptionParser(usage,version="%prog " + __version__)
parser.add_option("-i","--input-file",action="store",type="string",dest="input_file",help="Input file in SAM format. Use \"-\" represents standard input [required]")
parser.add_option("-r","--refgene",action="store",type="string",dest="ref_gene_model",help="Reference gene model in bed format. [required]")
(options,args)=parser.parse_args()
if not (options.input_file and options.ref_gene_model):
parser.print_help()
sys.exit(0)
if not os.path.exists(options.ref_gene_model):
print >>sys.stderr, '\n\n' + options.ref_gene_model + " does NOT exists" + '\n'
#parser.print_help()
sys.exit(0)
if os.path.exists(options.input_file):
file_obj=open(options.input_file)
pass
elif options.input_file == '-':
file_obj=sys.stdin
pass
else:
print >>sys.stderr, '\n\n' + options.input_file + " does NOT exists" + '\n'
#parser.print_help()
sys.exit(0)
print >>sys.stderr, "processing " + options.ref_gene_model + ' ...',
obj = BED.ParseBED(options.ref_gene_model)
utr_3 = obj.getUTR(utr=3)
utr_5 = obj.getUTR(utr=5)
cds_exon = obj.getCDSExon()
intron = obj.getIntron()
intron = BED.unionBed3(intron)
cds_exon=BED.unionBed3(cds_exon)
utr_5 = BED.unionBed3(utr_5)
utr_3 = BED.unionBed3(utr_3)
utr_5 = BED.subtractBed3(utr_5,cds_exon)
utr_3 = BED.subtractBed3(utr_3,cds_exon)
intron = BED.subtractBed3(intron,cds_exon)
intron = BED.subtractBed3(intron,utr_5)
intron = BED.subtractBed3(intron,utr_3)
intergenic_up_1kb = obj.getIntergenic(direction="up",size=1000)
intergenic_down_1kb = obj.getIntergenic(direction="down",size=1000)
intergenic_up_5kb = obj.getIntergenic(direction="up",size=5000)
intergenic_down_5kb = obj.getIntergenic(direction="down",size=5000)
intergenic_up_10kb = obj.getIntergenic(direction="up",size=10000)
intergenic_down_10kb = obj.getIntergenic(direction="down",size=10000)
#merge integenic region
intergenic_up_1kb=BED.unionBed3(intergenic_up_1kb)
intergenic_up_5kb=BED.unionBed3(intergenic_up_5kb)
intergenic_up_10kb=BED.unionBed3(intergenic_up_10kb)
intergenic_down_1kb=BED.unionBed3(intergenic_down_1kb)
intergenic_down_5kb=BED.unionBed3(intergenic_down_5kb)
intergenic_down_10kb=BED.unionBed3(intergenic_down_10kb)
#purify intergenic region
intergenic_up_1kb=BED.subtractBed3(intergenic_up_1kb,cds_exon)
intergenic_up_1kb=BED.subtractBed3(intergenic_up_1kb,utr_5)
intergenic_up_1kb=BED.subtractBed3(intergenic_up_1kb,utr_3)
intergenic_up_1kb=BED.subtractBed3(intergenic_up_1kb,intron)
intergenic_down_1kb=BED.subtractBed3(intergenic_down_1kb,cds_exon)
intergenic_down_1kb=BED.subtractBed3(intergenic_down_1kb,utr_5)
intergenic_down_1kb=BED.subtractBed3(intergenic_down_1kb,utr_3)
intergenic_down_1kb=BED.subtractBed3(intergenic_down_1kb,intron)
#purify intergenic region
intergenic_up_5kb=BED.subtractBed3(intergenic_up_5kb,cds_exon)
intergenic_up_5kb=BED.subtractBed3(intergenic_up_5kb,utr_5)
intergenic_up_5kb=BED.subtractBed3(intergenic_up_5kb,utr_3)
intergenic_up_5kb=BED.subtractBed3(intergenic_up_5kb,intron)
intergenic_down_5kb=BED.subtractBed3(intergenic_down_5kb,cds_exon)
intergenic_down_5kb=BED.subtractBed3(intergenic_down_5kb,utr_5)
intergenic_down_5kb=BED.subtractBed3(intergenic_down_5kb,utr_3)
intergenic_down_5kb=BED.subtractBed3(intergenic_down_5kb,intron)
#purify intergenic region
intergenic_up_10kb=BED.subtractBed3(intergenic_up_10kb,cds_exon)
intergenic_up_10kb=BED.subtractBed3(intergenic_up_10kb,utr_5)
intergenic_up_10kb=BED.subtractBed3(intergenic_up_10kb,utr_3)
intergenic_up_10kb=BED.subtractBed3(intergenic_up_10kb,intron)
intergenic_down_10kb=BED.subtractBed3(intergenic_down_10kb,cds_exon)
intergenic_down_10kb=BED.subtractBed3(intergenic_down_10kb,utr_5)
intergenic_down_10kb=BED.subtractBed3(intergenic_down_10kb,utr_3)
intergenic_down_10kb=BED.subtractBed3(intergenic_down_10kb,intron)
print >>sys.stderr, "Done"
ranges={}
totalReads=0
spliceReads=0
cUR=0
multiMapReads=0
print >>sys.stderr, "reading SAM file",
for line in file_obj:
if line.startswith("@"):continue
fields=line.rstrip('\n ').split()
flagCode=string.atoi(fields[1])
if (flagCode & 0x0004) != 0: continue #skip unmap reads
totalReads +=1
if not SAM.ParseSAM._uniqueHit_pat.search(line): #skip multiple mapped reads
multiMapReads +=1
continue
chrom = fields[2].upper()
chromStart = string.atoi(fields[3])-1
comb=[int(i) for i in SAM.ParseSAM._splicedHit_pat.findall(fields[5])] #"9M4721N63M3157N8M" return ['9', '4721', '63', '3157', '8']
cUR += (len(comb) +1)/2
if(len(comb)>1):
spliceReads += 1
blockStart=[]
blockSize=[]
for i in range(0,len(comb),2):
blockStart.append(chromStart + sum(comb[:i]) )
for i in range(0,len(comb),2):
blockSize.append(comb[i])
for st,size in zip(blockStart,blockSize):
mid = int(st) + (size/2)
if chrom not in ranges:
ranges[chrom] = Intersecter()
else:
ranges[chrom].add_interval( Interval( mid, mid ) )
print >>sys.stderr, "Done"
print >>sys.stderr, "Total Reads: " + str(totalReads)
print >>sys.stderr, "Multiple Hits: " + str(multiMapReads)
print >>sys.stderr, "Unique Hits: " + str(totalReads-multiMapReads)
print >>sys.stderr, "Spliced Hits: " + str(spliceReads)
print >>sys.stderr, "Total fragments: " + str(cUR)
print >>sys.stderr, "\nAssignning reads ...",
intron_read=0
intron_base=0
cds_exon_read=0
cds_exon_base=0
utr_5_read=0
utr_5_base=0
utr_3_read=0
utr_3_base=0
intergenic_up1kb_base=0
intergenic_up1kb_read=0
intergenic_down1kb_base=0
intergenic_down1kb_read=0
intergenic_up5kb_base=0
intergenic_up5kb_read=0
intergenic_down5kb_base=0
intergenic_down5kb_read=0
intergenic_up10kb_base=0
intergenic_up10kb_read=0
intergenic_down10kb_base=0
intergenic_down10kb_read=0
(intron_base,intron_read) = base_read(intron,ranges)
(cds_exon_base,cds_exon_read) = base_read(cds_exon,ranges)
(utr_5_base,utr_5_read) = base_read(utr_5,ranges)
(utr_3_base,utr_3_read) = base_read(utr_3,ranges)
(intergenic_up1kb_base, intergenic_up1kb_read) = base_read(intergenic_up_1kb,ranges)
(intergenic_up5kb_base, intergenic_up5kb_read) = base_read(intergenic_up_5kb,ranges)
(intergenic_up10kb_base, intergenic_up10kb_read) = base_read(intergenic_up_10kb,ranges)
(intergenic_down1kb_base, intergenic_down1kb_read) = base_read(intergenic_down_1kb,ranges)
(intergenic_down5kb_base, intergenic_down5kb_read) = base_read(intergenic_down_5kb,ranges)
(intergenic_down10kb_base, intergenic_down10kb_read) = base_read(intergenic_down_10kb,ranges)
print >>sys.stderr, "Done"
print >>sys.stderr, "========================================================="
print >>sys.stderr, "Group\tTotal_bases\tReads_count\tReads/Kb"
print >>sys.stderr, "CDS Exons:\t%d\t%d\t%5.2f" % (cds_exon_base,cds_exon_read,cds_exon_read*1000.0/cds_exon_base)
print >>sys.stderr, "5'UTR Exons:\t%d\t%d\t%5.2f" % (utr_5_base,utr_5_read, utr_5_read*1000.0/utr_5_base)
print >>sys.stderr, "3'UTR Exons:\t%d\t%d\t%5.2f" % (utr_3_base,utr_3_read, utr_3_read*1000.0/utr_3_base)
print >>sys.stderr, "Intronic region:\t%d\t%d\t%5.2f" % (intron_base,intron_read,intron_read*1000.0/intron_base)
print >>sys.stderr, "TSS up 1kb:\t%d\t%d\t%5.2f" % (intergenic_up1kb_base, intergenic_up1kb_read, intergenic_up1kb_read*1000.0/intergenic_up1kb_base)
print >>sys.stderr, "TSS up 5kb:\t%d\t%d\t%5.2f" % (intergenic_up5kb_base, intergenic_up5kb_read, intergenic_up5kb_read*1000.0/intergenic_up5kb_base)
print >>sys.stderr, "TSS up 10kb:\t%d\t%d\t%5.2f" % (intergenic_up10kb_base, intergenic_up10kb_read, intergenic_up10kb_read*1000.0/intergenic_up10kb_base)
print >>sys.stderr, "TES down 1kb:\t%d\t%d\t%5.2f" % (intergenic_down1kb_base, intergenic_down1kb_read, intergenic_down1kb_read*1000.0/intergenic_down1kb_base)
print >>sys.stderr, "TES down 5kb:\t%d\t%d\t%5.2f" % (intergenic_down5kb_base, intergenic_down5kb_read, intergenic_down5kb_read*1000.0/intergenic_down5kb_base)
print >>sys.stderr, "TES down 10kb:\t%d\t%d\t%5.2f" % (intergenic_down10kb_base, intergenic_down10kb_read, intergenic_down10kb_read*1000.0/intergenic_down10kb_base)
print >>sys.stderr, "========================================================="
