def main(argv=None):
options, args = process_command_line(argv)
f_gene = args[0]
assert os.path.exists(f_gene)
outhandle = sys.stdout
if options.outfile:
outfile = options.outfile
outhandle = open(outfile, "w")
llexons = set()
for gr in reader_gene(open(f_gene), 'bed'):
chrom = gr.get_chrom()
exons = gr.get_exons()
strand = gr.get_strand()
if strand == "+":
llexons.add((chrom, exons[-1][0], exons[-1][1], strand))
else:
llexons.add((chrom, exons[0][0], exons[0][1], strand))
i = 0
for chrom, s, e, strand in sorted(llexons):
i += 1
outhandle.write("\t".join(map(str, [
chrom, s, e, i, e - s, strand]))+"\n")
if options.outfile:
outhandle.close()
def read_gene(fh):
"""Return dict of gene_id:gene object, require name fields are unique"""
id2gene = {}
for gene in reader_gene(fh):
id2gene[gene.get_name()] = gene
return id2gene
def main(argv=None):
options, args = process_command_line(argv)
f_gene = args[0]
assert os.path.exists(f_gene)
outhandle = sys.stdout
if options.outfile:
outfile = options.outfile
outhandle = open(outfile, "w")
cinfo = {}
if options.genome:
for line in open(options.genome):
chrom, size = line.strip().split("\t")[:2]
cinfo[chrom] = int(size)
for gr in reader_gene(open(f_gene), 'bed'):
chrom = gr.get_chrom()
if gr.get_strand() == "+":
tes = gr.get_txEnd()
s = tes - options.len_up
e = tes + options.len_dn
else:
tes = gr.get_txStart()
s = tes - options.len_dn
e = tes + options.len_up
if chrom in cinfo:
e = min(e, cinfo[chrom])
s = max(s, 0)
if s >= e:
continue
outhandle.write("\t".join(map(str, [
chrom, s, e, gr.get_score(), tes, gr.get_strand()]))+"\n")
if options.outfile:
outhandle.close()
