def run(args):
# logging.basicConfig(level=logging.DEBUG)
dbi = DBI.init(args.bam, "bam")
out = IO.fopen(args.output, "w")
for i in TableIO.parse(IO.fopen(args.input, "r"), "bed12"):
print("QR\t", i, file=out)
for j in dbi.query(i, method="bam1", strand=args.strand):
if compatible_with_transcript(j, i):
print("HT\t{}".format(_translate_to_meta(i, j)), file=out)
elif not args.hit:
print("OP\t{}".format(j), file=out)
print("", file=out)
def count_list(beds,bin_num,strand):
bin_sum=[0.0 for i in xrange(bin_num)]
neg_bin_sum=[0.0 for i in xrange(bin_num)]
bin_dis=[[] for i in xrange(bin_num)]
neg_bin_dis=[[] for i in xrange(bin_num)]
for bed in beds:
neg_bed=bed._replace(strand=reverse_strand(bed.strand))
bed_bin=[0.0 for i in xrange(bin_num)]
neg_bed_bin=[0.0 for i in xrange(bin_num)]
for read in bam.query(bed,"bam1",strand=strand):
cdna_length=bed.cdna_length()
bin_step=float(cdna_length)/bin_num
if compatible_with_transcript(read,bed):
gene_bed=_translate(bed,read)
bin_start=gene_bed.start*bin_num/cdna_length
bin_stop=(gene_bed.stop-1)*bin_num/cdna_length
if bin_stop==bin_start:
bed_bin[bin_start]+=float(gene_bed.stop-gene_bed.start)/bin_step
else:
bed_bin[bin_start]+=bin_start+1-float(gene_bed.start)/bin_step
bed_bin[bin_stop]+=float(gene_bed.stop)/bin_step-bin_stop
for i in xrange(bin_start+1,bin_stop):
bed_bin[i]+=1.0
elif compatible_with_transcript(read,neg_bed):
gene_bed=_translate(bed,read)
bin_start=gene_bed.start*bin_num/cdna_length
bin_stop=(gene_bed.stop-1)*bin_num/cdna_length
if bin_stop==bin_start:
neg_bed_bin[bin_start]+=float(gene_bed.stop-gene_bed.start)/bin_step
else:
neg_bed_bin[bin_start]+=bin_start+1-float(gene_bed.start)/bin_step
neg_bed_bin[bin_stop]+=float(gene_bed.stop)/bin_step-bin_stop
for i in xrange(bin_start+1,bin_stop):
neg_bed_bin[i]+=1.0
for i in xrange(bin_num):
bin_sum[i]+=bed_bin[i]
neg_bin_sum[i]+=neg_bed_bin[i]
bin_dis[i].append(int(bed_bin[i]))
neg_bin_dis[i].append(int(neg_bed_bin[i]))
return bin_sum,bin_dis,neg_bin_sum,neg_bin_dis
def run(args):
#logging.basicConfig(level=logging.DEBUG)
dbi=DBI.init(args.bam,"bam")
mapped=dbi.mapped
out=IO.fopen(args.output,"w")
print("Gene\tRPKM",file=out);
for i in TableIO.parse(IO.fopen(args.input,"r"),"bed12"):
print(i.id,"\t",end="",file=out)
s=0.0
l=i.cdna_length()
if args.uniq:
for j in dbi.query(i,method="bam1",strand=args.strand,uniq=args.uniq):
if compatible_with_transcript(j,i):
s+=1.0
else:
for j in dbi.query(i,method="bam1",strand=args.strand,uniq=args.uniq):
if compatible_with_transcript(j,i):
(nh,_,_)=j.itemRgb.split(",")
nh=int(nh)
s+=1.0/nh
rpkm=float(s)*(1000000.0/mapped)*(1000.0/float(l))
print(rpkm,file=out)
def run(args):
if os.path.isfile(args.bed + ".tbi"):
dbi = DBI.init(args.bed, "tabix", cls=BED12)
else:
dbi = DBI.init(args.bed, "binindex", cls=BED12)
out = IO.fopen(args.output, "w")
for i in TableIO.parse(IO.fopen(args.input, "r"), "bed12"):
print("QR\t", i, file=out)
for j in dbi.query(i):
if compatible_with_transcript(j, i):
print("HT\t{}".format(_translate_to_meta(i, j)), file=out)
elif not args.hit:
print("OP\t{}".format(j), file=out)
print("", file=out)
