def do_buffer(buffer, txome, args):
results = []
for line_z in buffer:
z = line_z[1]
line = line_z[0]
gpd = GPD(line)
v = annotate_line(gpd, txome, args)
if not v: continue
type = 'partial'
if v[0]: type = 'full'
exon_count = v[2]
most_consecutive_exons = v[3]
read_exon_count = v[4]
tx_exon_count = v[5]
overlap_size = v[6]
read_length = v[7]
tx_length = v[8]
results.append(str(z)+"\t"+gpd.get_gene_name()+"\t"+v[9].get_gene_name()+"\t"+v[9].get_transcript_name()+"\t"+type+"\t"+\
str(exon_count)+"\t"+str(most_consecutive_exons)+"\t"+str(read_exon_count)+"\t"+str(tx_exon_count)+"\t"+\
str(overlap_size)+"\t"+str(read_length)+"\t"+str(tx_length)+"\t"+gpd.get_range().get_range_string()+"\t"+v[9].get_range().get_range_string()+"\t"+str(v[9].get_payload())+"\n")
return results
def main():
#do our inputs
args = do_inputs()
sys.stderr.write("Reading reference genepred\n")
ref = {}
tx_strand = {}
z = 0
with open(args.reference_genepred) as inf:
for line in inf:
gpd = GPD(line)
gname = gpd.get_gene_name()
tname = gpd.get_transcript_name()
tx_strand[tname] = gpd.get_strand()
if gname not in ref: ref[gname] = []
ref[gname].append(gpd)
z += 1
sys.stderr.write("Read "+str(len(ref.keys()))+" genes and "+str(z)+" transcripts\n")
if args.maximum_isoforms > 0:
sys.stderr.write("Removing genes with more than "+str(args.maximum_isoforms)+" isoforms.\n")
for gname in ref.keys():
if len(ref[gname]) > args.maximum_isoforms: del ref[gname]
sys.stderr.write("Now have "+str(len(ref.keys()))+" genes and "+str(sum([len(ref[x]) for x in ref.keys()]))+" transcripts\n")
sys.stderr.write("Filtering by length "+str(args.minimum_length)+" bp\n")
for gname in ref.keys():
passing = []
for gpd in ref[gname]:
if gpd.get_length() < args.minimum_length: continue
passing.append(gpd)
if len(passing) == 0: del ref[gname]
else: ref[gname] = passing
sys.stderr.write("Now have "+str(len(ref.keys()))+" genes and "+str(sum([len(ref[x]) for x in ref.keys()]))+" transcripts\n")
sys.stderr.write("Converting gpd into exon bed\n")
beds = []
for gname in ref.keys():
for gpd in ref[gname]:
tname = gpd.get_transcript_name()
for i in range(0,len(gpd.exons)):
ex = gpd.exons[i]
beds.append(ex.get_range().get_bed_array()+[gname,tname,i])
with open(args.tempdir+'/gpd.bed','w') as of:
for bed in sorted(beds,key=lambda x: (x[0],x[1],x[2],x[3],x[4],x[5])):
of.write("\t".join([str(x) for x in bed])+"\n")
sys.stderr.write("intersecting with bed depth\n")
of = open(args.tempdir+'/intersect.bed','w')
cmd = 'bedtools intersect -wo -a - -b '+args.tempdir+'/gpd.bed'
p = Popen(cmd.split(),stdin=args.bed_depth,stdout=of)
p.communicate()
coverage = {}
sys.stderr.write("Reading the intersection\n")
with open(args.tempdir+'/intersect.bed') as inf:
for line in inf:
f = line.rstrip().split("\t")
gname = f[7]
tname = f[8]
depth = int(f[3])
bed1 = Bed(f[0],int(f[1]),int(f[2]))
bed2 = Bed(f[4],int(f[5]),int(f[6]))
bed = bed1.union(bed2)
bed.set_payload(depth)
if gname not in coverage:
coverage[gname] = {}
if tname not in coverage[gname]:
coverage[gname][tname] = []
coverage[gname][tname].append(bed)
transcript_depths = {}
for gname in coverage:
for tname in coverage[gname]:
ref_gpd = [x for x in ref[gname] if x.get_transcript_name()==tname][0]
rlen = ref_gpd.get_length()
bases_covered = sum([x.length() for x in coverage[gname][tname]])
bases_area = sum([x.length()*x.get_payload() for x in coverage[gname][tname]])
avg_depth = float(bases_area)/float(rlen)
if avg_depth < args.minimum_average_depth: continue
if bases_covered < args.minimum_length: continue
#print gname
#print tname
#print rlen
#print bases_covered
#print bases_area
total_positions = {}
for ex in ref_gpd.exons:
b = ex.get_range().get_bed_array()
for i in range(b[1],b[2]):
total_positions[i] = 0 # zero indexed
for b in coverage[gname][tname]:
depth = b.get_payload()
barr = b.get_bed_array()
for i in range(barr[1],barr[2]):
total_positions[i] = depth
transcript_depths[tname] = total_positions
sys.stderr.write("have information needed to plot from "+str(len(transcript_depths.keys()))+" transcripts\n")
outputs = []
for tname in transcript_depths:
depths = transcript_depths[tname]
positions = sorted(depths.keys())
tx_len = len(positions)
bins = {}
for i in range(0,tx_len):
bin = int(100*float(i)/float(tx_len))
if bin not in bins: bins[bin] = []
bins[bin].append(depths[positions[i]])
for bin in bins:
bins[bin] = average(bins[bin])
biggest = float(max(bins.values()))
tx_array = [float(bins[x])/biggest for x in sorted(bins.keys())]
if tx_strand[tname] == '-':
tx_array.reverse()
#outputs.append(tx_array)
args.output.write(tname+"\t"+"\t".join([str(x) for x in tx_array])+"\n")
#for i in range(0,100):
# args.output.write("\t".join([str(x[i]) for x in outputs])+"\n")
args.output.close()
# Temporary working directory step 3 of 3 - Cleanup
if not args.specific_tempdir:
rmtree(args.tempdir)
