def make_gene_info(output_file, gene_model, genome_id, is_grc, add_ref_id):
# create UCSC to GRC chr name corresponding table
ucsc2grc = {}
if is_grc:
ucsc2grc = chr_name.make_ucsc2grc(genome_id)
ucsc_gene_file = utils.set_ucsc_gene_file(genome_id, gene_model)
hout = open(output_file + ".unsorted.tmp", 'w')
with gzip.open(ucsc_gene_file, 'r') as hin:
for line in hin:
F = line.rstrip('\n').split('\t')
chr = ucsc2grc[F[2]] if F[2] in ucsc2grc else F[2]
gene_id = F[1]
gene_start = F[4]
gene_end = F[5]
strand = F[3]
symbol = F[12]
exon_starts = F[9].split(',')
exon_ends = F[10].split(',')
gene_print_name = "---"
if gene_model == "refseq":
if add_ref_id:
gene_print_name = symbol + '(' + gene_id + ')'
else:
gene_print_name = symbol
elif gene_model == "gencode":
gene_print_name = gene_id
else:
print >> sys.stderr, "the value of gene_model should be refseq or gencode"
sys.exit(1)
key = chr + '\t' + gene_start + '\t' + gene_end
print >> hout, key + '\t' + gene_print_name + '\t' + "0" + '\t' + strand
hout.close()
hout = open(output_file + ".sorted.tmp", 'w')
subprocess.check_call(
["sort", "-k1,1", "-k2,2n", "-k3,3n", output_file + ".unsorted.tmp"],
stdout=hout)
hout.close()
hout = open(output_file, 'w')
subprocess.check_call(["bgzip", "-f", "-c", output_file + ".sorted.tmp"],
stdout=hout)
hout.close()
subprocess.check_call(["tabix", "-p", "bed", output_file])
subprocess.check_call(["rm", "-rf", output_file + ".unsorted.tmp"])
subprocess.check_call(["rm", "-rf", output_file + ".sorted.tmp"])
def make_simple_repeat_info(output_file, genome_id, is_grc):
# create UCSC to GRC chr name corresponding table
ucsc2grc = {}
if is_grc:
ucsc2grc = chr_name.make_ucsc2grc(genome_id)
if genome_id == "hg19":
simple_repeat_file = pkg_resources.resource_filename(
"annot_utils", "data/hg19/simpleRepeat.txt.gz")
elif genome_id == "hg38":
simple_repeat_file = pkg_resources.resource_filename(
"annot_utils", "data/hg38/simpleRepeat.txt.gz")
elif genome_id == "mm10":
simple_repeat_file = pkg_resources.resource_filename(
"annot_utils", "data/mm10/simpleRepeat.txt.gz")
else:
print >> sys.stderr, "genome_id shoud be hg19, hg38 or mm10"
sys.exit(1)
hout = open(output_file + ".unsorted.tmp", 'w')
with gzip.open(simple_repeat_file, 'r') as hin:
for line in hin:
F = line.rstrip('\n').split('\t')
chr = ucsc2grc[F[1]] if F[1] in ucsc2grc else F[1]
print >> hout, chr + '\t' + '\t'.join(F[2:])
hout.close()
hout = open(output_file + ".sorted.tmp", 'w')
subprocess.check_call(
["sort", "-k1,1", "-k2,2n", "-k3,3n", output_file + ".unsorted.tmp"],
stdout=hout)
hout.close()
hout = open(output_file, 'w')
subprocess.check_call(["bgzip", "-f", "-c", output_file + ".sorted.tmp"],
stdout=hout)
hout.close()
subprocess.check_call(["tabix", "-p", "bed", output_file])
subprocess.check_call(["rm", "-rf", output_file + ".unsorted.tmp"])
subprocess.check_call(["rm", "-rf", output_file + ".sorted.tmp"])
def make_exon_info(output_file, gene_model, genome_id, is_grc, add_ref_id):
# create UCSC to GRC chr name corresponding table
ucsc2grc = {}
if is_grc:
ucsc2grc = chr_name.make_ucsc2grc(genome_id)
ucsc_gene_file = utils.set_ucsc_gene_file(genome_id, gene_model)
hout = open(output_file + ".unsorted.tmp", 'w')
with gzip.open(ucsc_gene_file, 'r') as hin:
for line in hin:
F = line.rstrip('\n').split('\t')
chr = ucsc2grc[F[2]] if F[2] in ucsc2grc else F[2]
gene_id = F[1]
exon_starts = F[9].split(',')
exon_ends = F[10].split(',')
strand = F[3]
exonNum = int(F[8])
gene = F[1]
symbol = F[12]
size = 0
for i in range(len(exon_starts) - 1):
size = size + int(exon_ends[i]) - int(exon_starts[i])
gene_print_name = "---"
if gene_model == "refseq":
if add_ref_id:
gene_print_name = symbol + '(' + gene_id + ')'
else:
gene_print_name = symbol
elif gene_model == "gencode":
gene_print_name = gene_id
for i in range(0, len(exon_starts) - 1):
key = chr + '\t' + exon_starts[i] + '\t' + exon_ends[i]
if strand == "+":
print >> hout, key + '\t' + gene_print_name + '\t' + str(i) + '\t' + "+"
else:
print >> hout, key + '\t' + gene_print_name + '\t' + str(exonNum - i - 1) + '\t' + "-"
hout.close()
hout = open(output_file + ".sorted.tmp", 'w')
subprocess.check_call(["sort", "-k1,1", "-k2,2n", "-k3,3n", output_file + ".unsorted.tmp"], stdout = hout)
hout.close()
hout = open(output_file, 'w')
subprocess.check_call(["bgzip", "-f", "-c", output_file + ".sorted.tmp"], stdout = hout)
hout.close()
subprocess.check_call(["tabix", "-p", "bed", output_file])
subprocess.check_call(["rm", "-rf", output_file + ".unsorted.tmp"])
subprocess.check_call(["rm", "-rf", output_file + ".sorted.tmp"])
def make_boundary_info(output_file, genome_id, is_grc, donor_size,
acceptor_size):
# create UCSC to GRC chr name corresponding table
ucsc2grc = {}
if is_grc:
ucsc2grc = chr_name.make_ucsc2grc(genome_id)
ucsc_gene_file = utils.set_ucsc_gene_file(genome_id, "refseq")
donor_size_exon, donor_size_intron = [
int(x) for x in donor_size.split(',')
]
acceptor_size_intron, acceptor_size_exon = [
int(x) for x in acceptor_size.split(',')
]
key2junction, key2gene_id, key2exon_num = {}, {}, {}
with gzip.open(ucsc_gene_file, 'r') as hin:
for line in hin:
F = line.rstrip('\n').split('\t')
chr = ucsc2grc[F[2]] if F[2] in ucsc2grc else F[2]
starts = [int(x) for x in F[9].split(',') if x != '']
ends = [int(x) for x in F[10].split(',') if x != '']
strand = F[3]
exon_num = int(F[8])
gene_id = F[1]
symbol = F[12]
for i in range(0, exon_num - 1):
if strand == '+': # donor
key = '\t'.join([
chr,
str(ends[i] - donor_size_exon),
str(ends[i] + donor_size_intron), symbol, "donor",
strand
])
else: # acceptor
key = '\t'.join([
chr,
str(ends[i] - acceptor_size_exon),
str(ends[i] + acceptor_size_intron), symbol,
"acceptor", strand
])
junction = chr + ':' + str(
ends[i]) + '-' + str(starts[i + 1] + 1)
if key not in key2junction: key2junction[key] = []
if key not in key2gene_id: key2gene_id[key] = []
if key not in key2exon_num: key2exon_num[key] = []
key2junction[key].append(junction)
key2gene_id[key].append(gene_id)
key2exon_num[key].append(str(i))
for i in range(1, exon_num):
if strand == '+': # acceptor
key = '\t'.join([
chr,
str(starts[i] - acceptor_size_intron),
str(starts[i] + acceptor_size_exon), symbol,
"acceptor", strand
])
else: # donor
key = '\t'.join([
chr,
str(starts[i] - donor_size_intron),
str(starts[i] + donor_size_exon), symbol, "donor",
strand
])
junction = chr + ':' + str(
ends[i - 1]) + '-' + str(int(starts[i]) + 1)
if key not in key2junction: key2junction[key] = []
if key not in key2gene_id: key2gene_id[key] = []
if key not in key2exon_num: key2exon_num[key] = []
key2junction[key].append(junction)
key2gene_id[key].append(gene_id)
key2exon_num[key].append(str(i))
hout = open(output_file + ".unsorted.tmp", 'w')
for key in sorted(key2junction):
print >> hout, '\t'.join([
key, ','.join(key2junction[key]), ','.join(key2gene_id[key]),
','.join(key2exon_num[key])
])
hout.close()
hout = open(output_file + ".sorted.tmp", 'w')
subprocess.check_call(
["sort", "-k1,1", "-k2,2n", "-k3,3n", output_file + ".unsorted.tmp"],
stdout=hout)
hout.close()
hout = open(output_file, 'w')
subprocess.check_call(["bgzip", "-f", "-c", output_file + ".sorted.tmp"],
stdout=hout)
hout.close()
subprocess.check_call(["tabix", "-p", "bed", output_file])
subprocess.check_call(["rm", "-rf", output_file + ".unsorted.tmp"])
subprocess.check_call(["rm", "-rf", output_file + ".sorted.tmp"])