def rnaseq_vardict_variant_calling(data):
sample = dd.get_sample_name(data)
variation_dir = os.path.join(dd.get_work_dir(data), "variation")
safe_makedir(variation_dir)
out_file = os.path.join(variation_dir, sample + "-vardict.vcf.gz")
if file_exists(out_file):
data = dd.set_vrn_file(data, out_file)
return data
vardict_cmd = vardict.get_vardict_command(data)
strandbias = "teststrandbias.R"
var2vcf = "var2vcf_valid.pl"
vcfstreamsort = config_utils.get_program("vcfstreamsort", data)
compress_cmd = "| bgzip -c"
freq = float(dd.get_min_allele_fraction(data, 20) / 100.0)
var2vcf_opts = "-v 50"
fix_ambig = vcfutils.fix_ambiguous_cl()
remove_dup = vcfutils.remove_dup_cl()
r_setup = ("unset R_HOME && export PATH=%s:$PATH && "
% os.path.dirname(Rscript_cmd()))
ref_file = dd.get_ref_file(data)
bamfile = dd.get_work_bam(data)
bed_file = gtf.gtf_to_bed(dd.get_gtf_file(data))
opts = " -c 1 -S 2 -E 3 -g 4 "
with file_transaction(out_file) as tx_out_file:
jvm_opts = vardict._get_jvm_opts(data, tx_out_file)
cmd = ("{r_setup}{jvm_opts}{vardict_cmd} -G {ref_file} -f {freq} "
"-N {sample} -b {bamfile} {opts} {bed_file} "
"| {strandbias}"
"| {var2vcf} -N {sample} -E -f {freq} {var2vcf_opts} "
"| {fix_ambig} | {remove_dup} | {vcfstreamsort} {compress_cmd} "
"> {tx_out_file}")
message = "Calling RNA-seq variants with VarDict"
do.run(cmd.format(**locals()), message)
data = dd.set_vrn_file(data, out_file)
return data
def ensure_annotations(resources, data):
"""Prepare any potentially missing annotations for downstream processing in a local directory.
"""
transcript_gff = tz.get_in(["rnaseq", "transcripts"], resources)
if transcript_gff and utils.file_exists(transcript_gff):
out_dir = os.path.join(tz.get_in(["dirs", "work"], data),
"inputs", "data", "annotations")
resources["rnaseq"]["gene_bed"] = gtf.gtf_to_bed(transcript_gff, out_dir)
return resources
def _ensure_annotations(resources, data):
"""Prepare any potentially missing annotations for downstream processing in a local directory.
"""
transcript_gff = tz.get_in(["rnaseq", "transcripts"], resources)
if transcript_gff and utils.file_exists(transcript_gff):
out_dir = utils.safe_makedir(os.path.join(tz.get_in(["dirs", "work"], data),
"inputs", "data", "annotations"))
resources["rnaseq"]["gene_bed"] = gtf.gtf_to_bed(transcript_gff, out_dir)
return resources
def _setup_variant_regions(data):
"""Ensure we have variant regions for calling, using transcript if not present.
Respects noalt_calling by removing additional contigs to improve
speeds.
"""
vr_file = dd.get_variant_regions(data)
if not vr_file:
vr_file = gtf.gtf_to_bed(dd.get_gtf_file(data))
contigs = set([c.name for c in ref.file_contigs(dd.get_ref_file(data))])
out_file = os.path.join(
utils.safe_makedir(os.path.join(dd.get_work_dir(data),
"bedprep")), "%s-rnaseq_clean.bed" %
utils.splitext_plus(os.path.basename(vr_file))[0])
if not utils.file_uptodate(out_file, vr_file):
with file_transaction(data, out_file) as tx_out_file:
with open(tx_out_file, "w") as out_handle:
with shared.bedtools_tmpdir(data):
for r in pybedtools.BedTool(vr_file):
if r.chrom in contigs:
if chromhacks.is_nonalt(r.chrom):
out_handle.write(str(r))
data = dd.set_variant_regions(data, out_file)
return data
