def _maybe_add_junction_files(algorithm, sample, out):
"""
add splice junction files from STAR, if available
"""
junction_bed = dd.get_junction_bed(sample)
if junction_bed:
out.append({
"path": junction_bed,
"type": "bed",
"ext": "SJ",
"dir": "STAR"
})
chimeric_file = dd.get_chimericjunction(sample)
if chimeric_file:
out.append({
"path": chimeric_file,
"type": "tsv",
"ext": "chimericSJ",
"dir": "STAR"
})
sj_file = dd.get_starjunction(sample)
if sj_file:
out.append({
"path": sj_file,
"type": "tab",
"ext": "SJ",
"dir": "STAR"
})
star_summary = dd.get_summary_qc(sample).get("star", None)
if star_summary:
star_log = star_summary["base"]
if star_log:
out.append({"path": star_log, "type": "log", "dir": "STAR"})
return out
def _maybe_add_junction_files(algorithm, sample, out):
"""
add splice junction files from STAR, if available
"""
junction_bed = dd.get_junction_bed(sample)
if junction_bed:
out.append({
"path": junction_bed,
"type": "bed",
"ext": "SJ",
"dir": "STAR"
})
chimeric_file = dd.get_chimericjunction(sample)
if chimeric_file:
out.append({
"path": chimeric_file,
"type": "tsv",
"ext": "chimericSJ",
"dir": "STAR"
})
sj_file = dd.get_starjunction(sample)
if sj_file:
out.append({
"path": sj_file,
"type": "tab",
"ext": "SJ",
"dir": "STAR"
})
return out
def filter_junction_variants(vrn_file, data):
"""
filter out variants within 10 basepairs of a splice junction, these are
very prone to being false positives with RNA-seq data
"""
SJ_BP_MASK = 10
vrn_dir = os.path.dirname(vrn_file)
splicebed = dd.get_junction_bed(data)
if not file_exists(splicebed):
logger.info(
"Splice junction BED file not found, skipping filtering of "
"variants closed to splice junctions.")
return vrn_file
spliceslop = get_padded_bed_file(vrn_dir, splicebed, SJ_BP_MASK, data)
out_file = os.path.splitext(vrn_file)[0] + "-junctionfiltered.vcf.gz"
if file_exists(out_file):
return out_file
with file_transaction(data, out_file) as tx_out_file:
out_base = os.path.splitext(tx_out_file)[0]
logger.info(
"Removing variants within %d bases of splice junctions listed in %s from %s. "
% (SJ_BP_MASK, spliceslop, vrn_file))
pybedtools.BedTool(vrn_file).intersect(spliceslop,
wa=True,
header=True,
v=True).saveas(out_base)
tx_out_file = vcfutils.bgzip_and_index(out_base, dd.get_config(data))
return out_file
def filter_junction_variants(vrn_file, data):
"""
filter out variants within 10 basepairs of a splice junction, these are
very prone to being false positives with RNA-seq data
"""
SJ_BP_MASK = 10
vrn_dir = os.path.dirname(vrn_file)
splicebed = dd.get_junction_bed(data)
if not file_exists(splicebed):
logger.info("Splice junction BED file not found, skipping filtering of "
"variants closed to splice junctions.")
return vrn_file
spliceslop = get_padded_bed_file(vrn_dir, splicebed, SJ_BP_MASK, data)
out_file = os.path.splitext(vrn_file)[0] + "-junctionfiltered.vcf.gz"
if file_exists(out_file):
return out_file
with file_transaction(data, out_file) as tx_out_file:
out_base = os.path.splitext(tx_out_file)[0]
logger.info("Removing variants within %d bases of splice junctions listed in %s from %s. " % (SJ_BP_MASK, spliceslop, vrn_file))
pybedtools.BedTool(vrn_file).intersect(spliceslop, wa=True, header=True, v=True).saveas(out_base)
tx_out_file = vcfutils.bgzip_and_index(out_base, dd.get_config(data))
return out_file
