def run(args):
logging.basicConfig(level=logging.DEBUG)
fin=IO.fopen(args.input,"r")
out=IO.fopen(args.output,"w")
bam=DBI.init(args.bam,"bam");
beds=[i for i in TableIO.parse(fin,"bed12")]
beds.sort()
bp=args.bp
print("mapped:{}".format(bam.mapped))
print("unmapped:{}".format(bam.unmapped))
data={}
for i,x in enumerate(iter_cluster(beds)):
print("{}\t{}:{}-{}".format(i+1,x["chr"],x["start"]+1,x["stop"]))
'''
cds=[z.cds() for z in x["beds"] if z.cds()]
utr3=[z.utr3() for z in x["beds"] if z.utr3()]
utr5=[z.utr5() for z in x["beds"] if z.utr5()]
'''
coords = [ up_down_coordinate(gene,args.bp,args.bp) for gene in x["beds"] ]
for j,y in enumerate(coords):
data[y.id]={}
data[y.id]["coord"]=y
data[y.id]["values"]=[0.0 for l in range(y.cdna_length())];
coord_beds = [ _translate(coord,bed) for coord,bed in itertools.izip(coords,x["beds"])]
for j,read in enumerate(bam.query(method="bam1",chr=x["chr"],start=x["start"]-args.bp,stop=x["stop"]+args.bp,strand=args.strand)):
NM=getNM(read) # number of hits
NC=0 # number of compatible
c_coords=[]
for k,coord in enumerate(coords):
if overlap(read,coord) and compatible(read,coord): # don't consider the reads extend out of coords.
NC+=1
c_coords.append(k)
for k,c in enumerate(c_coords):
coord=coords[c]
if read.start < coord.start or read.stop > coord.stop:
start=max(read.start,coord.start)
stop=min(read.stop,coord.stop)
read=read._slice(start,stop)
read_in_coord = _translate(coord,read)
for l in xrange(read_in_coord.start,read_in_coord.stop):
data[coord.id]["values"][l]+=1.0/NC/NM
for j,y in enumerate(coords):
print(data[y.id]["coord"])
print(data[y.id]["values"])
'''
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
