def get_sv_bed(data, method=None, out_dir=None, include_gene_names=True):
"""Retrieve a BED file of regions for SV and heterogeneity calling using the provided method.
method choices:
- exons: Raw BED file of exon regions
- transcripts: Full collapsed regions with the min and max of each transcript.
- transcriptsXXXX: Collapsed regions around transcripts with a window size of
XXXX.
- A custom BED file of regions
"""
if method is None:
method = tz.get_in(["config", "algorithm", "sv_regions"],
data) or dd.get_variant_regions(data)
gene_file = dd.get_gene_bed(data)
if method and os.path.isfile(method):
return method
elif not gene_file or not method:
return None
elif method == "exons":
return gene_file
elif method.startswith("transcripts"):
window = method.split("transcripts")[-1]
window = int(float(window)) if window else 0
return _collapse_transcripts(gene_file,
window,
data,
out_dir,
include_gene_names=include_gene_names)
else:
raise ValueError("Unexpected transcript retrieval method: %s" % method)
def add_genes(in_file, data, max_distance=10000):
"""Add gene annotations to a BED file from pre-prepared RNA-seq data.
max_distance -- only keep annotations within this distance of event
"""
import pybedtools
gene_file = dd.get_gene_bed(data)
if gene_file and utils.file_exists(in_file):
out_file = "%s-annotated.bed" % utils.splitext_plus(in_file)[0]
if not utils.file_uptodate(out_file, in_file):
input_rec = iter(pybedtools.BedTool(in_file)).next()
# keep everything after standard chrom/start/end, 1-based
extra_fields = range(4, len(input_rec.fields) + 1)
# keep the new gene annotation
gene_index = len(input_rec.fields) + 4
extra_fields.append(gene_index)
columns = ",".join([str(x) for x in extra_fields])
max_column = max(extra_fields) + 1
ops = ",".join(["distinct"] * len(extra_fields))
with file_transaction(data, out_file) as tx_out_file:
# swap over gene name to '.' if beyond maximum distance
# cut removes the last distance column which can cause issues
# with bedtools merge: 'ERROR: illegal character '.' found in integer conversion of string'
distance_filter = (r"""awk -F$'\t' -v OFS='\t' '{if ($NF > %s) $%s = "."} {print}'""" %
(max_distance, gene_index))
cmd = ("sort -k1,1 -k2,2n {in_file} | "
"bedtools closest -d -t all -a - -b {gene_file} | "
"{distance_filter} | cut -f 1-{max_column} | "
"bedtools merge -i - -c {columns} -o {ops} -delim ';' > {tx_out_file}")
do.run(cmd.format(**locals()), "Annotate BED file with gene info")
return out_file
else:
return in_file
def get_sv_bed(data, method=None, out_dir=None, include_gene_names=True):
"""Retrieve a BED file of regions for SV and heterogeneity calling using the provided method.
method choices:
- exons: Raw BED file of exon regions
- transcripts: Full collapsed regions with the min and max of each transcript.
- transcriptsXXXX: Collapsed regions around transcripts with a window size of
XXXX.
- A custom BED file of regions
"""
if method is None:
method = tz.get_in(["config", "algorithm", "sv_regions"], data)
gene_file = dd.get_gene_bed(data)
if method and os.path.isfile(method):
return method
elif not gene_file or not method:
return None
elif method == "exons":
return gene_file
elif method.startswith("transcripts"):
window = method.split("transcripts")[-1]
window = int(float(window)) if window else 0
return _collapse_transcripts(gene_file, window, data, out_dir, include_gene_names=include_gene_names)
else:
raise ValueError("Unexpected transcript retrieval method: %s" % method)
def subset_by_genes(in_file, data, out_dir, pad):
"""Subset BED file of regions to only those within pad of the final output.
"""
gene_file = dd.get_gene_bed(data)
fai_file = ref.fasta_idx(dd.get_ref_file(data))
if not gene_file or not utils.file_exists(in_file):
return in_file
else:
out_file = os.path.join(out_dir, "%s-geneonly.bed" % utils.splitext_plus(os.path.basename(in_file))[0])
if not utils.file_uptodate(out_file, in_file):
with file_transaction(data, out_file) as tx_out_file:
want_region_file = "%s-targetregions%s" % utils.splitext_plus(out_file)
pybedtools.BedTool(gene_file).slop(g=fai_file, b=pad).merge().saveas(want_region_file)
pybedtools.BedTool(in_file).intersect(b=want_region_file).sort().saveas(tx_out_file)
return out_file
