def _combine_files(tsv_files, work_dir, data):
"""Combine multiple priority tsv files into a final sorted output.
"""
header = "\t".join(
[
"caller",
"sample",
"chrom",
"start",
"end",
"svtype",
"known",
"lof",
"annotation",
"split_read_support",
"paired_end_support",
]
)
sample = dd.get_sample_name(data)
out_file = os.path.join(work_dir, "%s-prioritize.tsv" % (sample))
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
input_files = " ".join(tsv_files)
sort_cmd = bedutils.get_sort_cmd()
cmd = "{{ echo '{header}'; cat {input_files} | {sort_cmd} -k3,3 -k4,4n; }} > {tx_out_file}"
do.run(cmd.format(**locals()), "Combine prioritized from multiple callers")
return out_file
def _add_genes_to_bed(in_file, gene_file, fai_file, out_file, data, max_distance=10000):
"""Re-usable subcomponent that annotates BED file genes from another BED
"""
try:
input_rec = iter(pybedtools.BedTool(in_file)).next()
except StopIteration: # empty file
utils.copy_plus(in_file, out_file)
return
# 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))
# 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))
sort_cmd = bedutils.get_sort_cmd()
cat_cmd = "zcat" if in_file.endswith(".gz") else "cat"
# Ensure gene transcripts match reference genome
ready_gene_file = os.path.join(os.path.dirname(out_file), "%s-genomeonly.bed" %
(utils.splitext_plus(os.path.basename(gene_file))[0]))
ready_gene_file = bedutils.subset_to_genome(gene_file, ready_gene_file, data)
cmd = ("{cat_cmd} {in_file} | grep -v ^track | grep -v ^browser | grep -v ^# | "
"{sort_cmd} -k1,1 -k2,2n | "
"bedtools closest -g <(cut -f1,2 {fai_file} | {sort_cmd} -k1,1 -k2,2n) "
"-d -t all -a - -b <({sort_cmd} -k1,1 -k2,2n {ready_gene_file}) | "
"{distance_filter} | cut -f 1-{max_column} | "
"bedtools merge -i - -c {columns} -o {ops} -delim ',' -d -10 > {out_file}")
do.run(cmd.format(**locals()), "Annotate BED file with gene info")
def _collapse_transcripts(in_file, window, data, out_dir):
"""Collapse transcripts into min/max coordinates and optionally add windows.
"""
if out_dir is None:
out_dir = os.path.dirname(in_file)
out_file = os.path.join(out_dir,
"%s-transcripts_w%s.bed" % (os.path.splitext(os.path.basename(in_file))[0],
window))
chrom_sizes = {}
for contig in ref.file_contigs(dd.get_ref_file(data), data["config"]):
chrom_sizes[contig.name] = contig.size
if not utils.file_uptodate(out_file, in_file):
with file_transaction(data, out_file) as tx_out_file:
prep_file = "%s-sortprep%s" % os.path.splitext(tx_out_file)
sort_cmd = bedutils.get_sort_cmd()
cmd = "{sort_cmd} -k4,4 -k1,1 {in_file} > {prep_file}"
do.run(cmd.format(**locals()), "Sort BED file by transcript name")
with open(tx_out_file, "w") as out_handle:
# Work around for segmentation fault issue with groupby
# https://github.com/daler/pybedtools/issues/131#issuecomment-89832476
x = pybedtools.BedTool(prep_file)
def gen():
for r in x:
yield r
for name, rs in itertools.groupby(gen(), lambda r: (r.name, r.chrom)):
rs = list(rs)
r = rs[0]
for gcoords in _group_coords(rs):
min_pos = max(min(gcoords) - window, 0)
max_pos = min(max(gcoords) + window, chrom_sizes[r.chrom])
out_handle.write("%s\t%s\t%s\t%s\n" % (r.chrom, min_pos, max_pos, r.name))
return bedutils.sort_merge(out_file, data)
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
"""
gene_file = regions.get_sv_bed(data, "exons", out_dir=os.path.dirname(in_file))
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))
fai_file = ref.fasta_idx(dd.get_ref_file(data))
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) $%s = "."} {print}'""" %
(max_distance, gene_index))
sort_cmd = bedutils.get_sort_cmd()
cmd = ("{sort_cmd} -k1,1 -k2,2n {in_file} | "
"bedtools closest -g <(cut -f1,2 {fai_file} | {sort_cmd} -k1,1 -k2,2n) "
"-d -t all -a - -b <({sort_cmd} -k1,1 -k2,2n {gene_file}) | "
"{distance_filter} | cut -f 1-{max_column} | "
"bedtools merge -i - -c {columns} -o {ops} -delim ',' > {tx_out_file}")
do.run(cmd.format(**locals()), "Annotate BED file with gene info")
return out_file
else:
return in_file
def add_genes_to_bed(in_file,
gene_file,
fai_file,
out_file,
max_distance=10000):
"""Re-usable subcomponent that annotates BED file genes from another BED
"""
input_rec = iter(pybedtools.BedTool(in_file)).next()
# keep everything after standard chrom/start/end, 1-based
extra_fields = range(4, len(input_rec.fields) + 1)
# keep the new gene annotation
gene_index = len(input_rec.fields) + 4
extra_fields.append(gene_index)
columns = ",".join([str(x) for x in extra_fields])
max_column = max(extra_fields) + 1
ops = ",".join(["distinct"] * len(extra_fields))
# swap over gene name to '.' if beyond maximum distance
# cut removes the last distance column which can cause issues
# with bedtools merge: 'ERROR: illegal character '.' found in integer conversion of string'
distance_filter = (
r"""awk -F$'\t' -v OFS='\t' '{if ($NF > %s) $%s = "."} {print}'""" %
(max_distance, gene_index))
sort_cmd = bedutils.get_sort_cmd()
cmd = (
"{sort_cmd} -k1,1 -k2,2n {in_file} | "
"bedtools closest -g <(cut -f1,2 {fai_file} | {sort_cmd} -k1,1 -k2,2n) "
"-d -t all -a - -b <({sort_cmd} -k1,1 -k2,2n {gene_file}) | "
"{distance_filter} | cut -f 1-{max_column} | "
"bedtools merge -i - -c {columns} -o {ops} -delim ',' > {out_file}")
do.run(cmd.format(**locals()), "Annotate BED file with gene info")
def _add_genes_to_bed(in_file, gene_file, fai_file, out_file, max_distance=10000):
"""Re-usable subcomponent that annotates BED file genes from another BED
"""
input_rec = iter(pybedtools.BedTool(in_file)).next()
# keep everything after standard chrom/start/end, 1-based
extra_fields = range(4, len(input_rec.fields) + 1)
# keep the new gene annotation
gene_index = len(input_rec.fields) + 4
extra_fields.append(gene_index)
columns = ",".join([str(x) for x in extra_fields])
max_column = max(extra_fields) + 1
ops = ",".join(["distinct"] * len(extra_fields))
# swap over gene name to '.' if beyond maximum distance
# cut removes the last distance column which can cause issues
# with bedtools merge: 'ERROR: illegal character '.' found in integer conversion of string'
distance_filter = (r"""awk -F$'\t' -v OFS='\t' '{if ($NF > %s) $%s = "."} {print}'""" %
(max_distance, gene_index))
sort_cmd = bedutils.get_sort_cmd()
cat_cmd = "zcat" if in_file.endswith(".gz") else "cat"
cmd = ("{cat_cmd} {in_file} | grep -v ^track | grep -v ^browser | grep -v ^# | "
"{sort_cmd} -k1,1 -k2,2n | "
"bedtools closest -g <(cut -f1,2 {fai_file} | {sort_cmd} -k1,1 -k2,2n) "
"-d -t all -a - -b <({sort_cmd} -k1,1 -k2,2n {gene_file}) | "
"{distance_filter} | cut -f 1-{max_column} | "
"bedtools merge -i - -c {columns} -o {ops} -delim ',' > {out_file}")
do.run(cmd.format(**locals()), "Annotate BED file with gene info")
def _combine_files(tsv_files, work_dir, data):
"""Combine multiple priority tsv files into a final sorted output.
"""
header = "\t".join(["caller", "sample", "chrom", "start", "end", "svtype",
"lof", "annotation", "split_read_support", "paired_support_PE", "paired_support_PR"])
sample = dd.get_sample_name(data)
out_file = os.path.join(work_dir, "%s-prioritize.tsv" % (sample))
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
input_files = " ".join(tsv_files)
sort_cmd = bedutils.get_sort_cmd()
cmd = "{{ echo '{header}'; cat {input_files} | {sort_cmd} -k3,3 -k4,4n; }} > {tx_out_file}"
do.run(cmd.format(**locals()), "Combine prioritized from multiple callers")
return out_file
def _group_by_ctype(bed_file, depth, region, region_file, out_file, data):
"""Group adjacent callable/uncallble regions into defined intervals.
Uses tips from bedtools discussion:
https://groups.google.com/d/msg/bedtools-discuss/qYDE6XF-GRA/2icQtUeOX_UJ
https://gist.github.com/arq5x/b67196a46db5b63bee06
"""
with file_transaction(data, out_file) as tx_out_file:
min_cov = depth["min"]
sort_cmd = bedutils.get_sort_cmd()
cmd = (r"""cat {bed_file} | awk '{{if ($4 == 0) {{print $0"\tNO_COVERAGE"}} """
r"""else if ($4 < {min_cov}) {{print $0"\tLOW_COVERAGE"}} """
r"""else {{print $0"\tCALLABLE"}} }}' | """
"bedtools groupby -prec 21 -g 1,5 -c 1,2,3,5 -o first,first,max,first | "
"cut -f 3-6 | "
"bedtools intersect -nonamecheck -a - -b {region_file} | "
"{sort_cmd} -k1,1 -k2,2n > {tx_out_file}")
do.run(cmd.format(**locals()), "bedtools groupby coverage: %s" % (str(region)), data)
def _group_by_ctype(bed_file, depth, region, region_file, out_file, data):
"""Group adjacent callable/uncallble regions into defined intervals.
Uses tips from bedtools discussion:
https://groups.google.com/d/msg/bedtools-discuss/qYDE6XF-GRA/2icQtUeOX_UJ
https://gist.github.com/arq5x/b67196a46db5b63bee06
"""
with file_transaction(data, out_file) as tx_out_file:
min_cov = depth["min"]
sort_cmd = bedutils.get_sort_cmd()
cmd = (
r"""cat {bed_file} | awk '{{if ($4 == 0) {{print $0"\tNO_COVERAGE"}} """
r"""else if ($4 < {min_cov}) {{print $0"\tLOW_COVERAGE"}} """
r"""else {{print $0"\tCALLABLE"}} }}' | """
"bedtools groupby -prec 21 -g 1,5 -c 1,2,3,5 -o first,first,max,first | "
"cut -f 3-6 | "
"bedtools intersect -nonamecheck -a - -b {region_file} | "
"{sort_cmd} -k1,1 -k2,2n > {tx_out_file}")
do.run(cmd.format(**locals()),
"bedtools groupby coverage: %s" % (str(region)), data)
def add_genes(in_file, data, max_distance=10000):
"""Add gene annotations to a BED file from pre-prepared RNA-seq data.
max_distance -- only keep annotations within this distance of event
"""
gene_file = regions.get_sv_bed(data,
"exons",
out_dir=os.path.dirname(in_file))
if gene_file and utils.file_exists(in_file):
out_file = "%s-annotated.bed" % utils.splitext_plus(in_file)[0]
if not utils.file_uptodate(out_file, in_file):
input_rec = iter(pybedtools.BedTool(in_file)).next()
# keep everything after standard chrom/start/end, 1-based
extra_fields = range(4, len(input_rec.fields) + 1)
# keep the new gene annotation
gene_index = len(input_rec.fields) + 4
extra_fields.append(gene_index)
columns = ",".join([str(x) for x in extra_fields])
max_column = max(extra_fields) + 1
ops = ",".join(["distinct"] * len(extra_fields))
fai_file = ref.fasta_idx(dd.get_ref_file(data))
with file_transaction(data, out_file) as tx_out_file:
# swap over gene name to '.' if beyond maximum distance
# cut removes the last distance column which can cause issues
# with bedtools merge: 'ERROR: illegal character '.' found in integer conversion of string'
distance_filter = (
r"""awk -F$'\t' -v OFS='\t' '{if ($NF > %s) $%s = "."} {print}'"""
% (max_distance, gene_index))
sort_cmd = bedutils.get_sort_cmd()
cmd = (
"{sort_cmd} -k1,1 -k2,2n {in_file} | "
"bedtools closest -g <(cut -f1,2 {fai_file} | {sort_cmd} -k1,1 -k2,2n) "
"-d -t all -a - -b <({sort_cmd} -k1,1 -k2,2n {gene_file}) | "
"{distance_filter} | cut -f 1-{max_column} | "
"bedtools merge -i - -c {columns} -o {ops} -delim ',' > {tx_out_file}"
)
do.run(cmd.format(**locals()),
"Annotate BED file with gene info")
return out_file
else:
return in_file
def _add_genes_to_bed(in_file, gene_file, fai_file, out_file, data, max_distance=10000):
"""Re-usable subcomponent that annotates BED file genes from another BED
"""
try:
input_rec = next(iter(pybedtools.BedTool(in_file)))
except StopIteration: # empty file
utils.copy_plus(in_file, out_file)
return
# keep everything after standard chrom/start/end, 1-based
extra_fields = list(range(4, len(input_rec.fields) + 1))
# keep the new gene annotation
gene_index = len(input_rec.fields) + 4
extra_fields.append(gene_index)
columns = ",".join([str(x) for x in extra_fields])
max_column = max(extra_fields) + 1
ops = ",".join(["distinct"] * len(extra_fields))
# swap over gene name to '.' if beyond maximum distance
# cut removes the last distance column which can cause issues
# with bedtools merge: 'ERROR: illegal character '.' found in integer conversion of string'
distance_filter = (r"""awk -F$'\t' -v OFS='\t' '{if ($NF > %s || $NF < -%s) $%s = "."} {print}'""" %
(max_distance, max_distance, gene_index))
sort_cmd = bedutils.get_sort_cmd(os.path.dirname(out_file))
cat_cmd = "zcat" if in_file.endswith(".gz") else "cat"
# Ensure gene transcripts match reference genome
ready_gene_file = os.path.join(os.path.dirname(out_file), "%s-genomeonly.bed" %
(utils.splitext_plus(os.path.basename(gene_file))[0]))
ready_gene_file = bedutils.subset_to_genome(gene_file, ready_gene_file, data)
exports = "export TMPDIR=%s && %s" % (os.path.dirname(out_file), utils.local_path_export())
bcbio_py = sys.executable
gsort = config_utils.get_program("gsort", data)
cmd = ("{exports}{cat_cmd} {in_file} | grep -v ^track | grep -v ^browser | grep -v ^# | "
"{bcbio_py} -c 'from bcbio.variation import bedutils; bedutils.remove_bad()' | "
"{gsort} - {fai_file} | "
"bedtools closest -g {fai_file} "
"-D ref -t first -a - -b <({gsort} {ready_gene_file} {fai_file}) | "
"{distance_filter} | cut -f 1-{max_column} | "
"bedtools merge -i - -c {columns} -o {ops} -delim ',' -d -10 > {out_file}")
do.run(cmd.format(**locals()), "Annotate BED file with gene info")
