def get_coords(data):
for category, vtypes in [("LOH", {"LOSS", "HETEROZYGOSITY"}),
("amplification", {"AMPLIFICATION"})]:
out = tz.get_in([category, dd.get_genome_build(data)], _COORDS, {})
priority_file = dd.get_svprioritize(data)
if priority_file and os.path.basename(priority_file).find("civic") >= 0:
for chrom, start, end, gene in _civic_regions(priority_file, vtypes, dd.get_disease(data)):
out[gene] = (chrom, start, end)
yield category, out
def get_coords(data):
"""Retrieve coordinates of genes of interest for prioritization.
Can read from CIViC input data or a supplied BED file of chrom, start, end
and gene information.
"""
for category, vtypes in [("LOH", {"LOSS", "HETEROZYGOSITY"}),
("amplification", {"AMPLIFICATION"})]:
out = tz.get_in([category, dd.get_genome_build(data)], _COORDS, {})
priority_file = dd.get_svprioritize(data)
if priority_file:
if os.path.basename(priority_file).find("civic") >= 0:
for chrom, start, end, gene in _civic_regions(priority_file, vtypes, dd.get_disease(data)):
out[gene] = (chrom, start, end)
elif os.path.basename(priority_file).find(".bed") >= 0:
for line in utils.open_gzipsafe(priority_file):
parts = line.strip().split("\t")
if len(parts) >= 4:
chrom, start, end, gene = parts[:4]
out[gene] = (chrom, int(start), int(end))
yield category, out
def get_coords(data):
"""Retrieve coordinates of genes of interest for prioritization.
Can read from CIViC input data or a supplied BED file of chrom, start, end
and gene information.
"""
for category, vtypes in [("LOH", {"LOSS", "HETEROZYGOSITY"}),
("amplification", {"AMPLIFICATION"})]:
out = tz.get_in([category, dd.get_genome_build(data)], _COORDS, {})
priority_file = dd.get_svprioritize(data)
if priority_file:
if os.path.basename(priority_file).find("civic") >= 0:
for chrom, start, end, gene in _civic_regions(
priority_file, vtypes, dd.get_disease(data)):
out[gene] = (chrom, start, end)
elif os.path.basename(priority_file).find(".bed") >= 0:
for line in utils.open_gzipsafe(priority_file):
parts = line.strip().split("\t")
if len(parts) >= 4:
chrom, start, end, gene = parts[:4]
out[gene] = (chrom, int(start), int(end))
yield category, out