def _amber_het_file(method, vrn_files, work_dir, paired):
"""Create file of BAFs in normal heterozygous positions compatible with AMBER.
Two available methods:
- pon -- Use panel of normals with likely heterozygous sites.
- variants -- Use pre-existing variant calls, filtered to likely heterozygotes.
https://github.com/hartwigmedical/hmftools/tree/master/amber
https://github.com/hartwigmedical/hmftools/blob/637e3db1a1a995f4daefe2d0a1511a5bdadbeb05/hmf-common/src/test/resources/amber/new.amber.baf
"""
assert vrn_files, "Did not find compatible variant calling files for PURPLE inputs"
from bcbio.heterogeneity import bubbletree
if method == "variants":
amber_dir = utils.safe_makedir(os.path.join(work_dir, "amber"))
out_file = os.path.join(amber_dir, "%s.amber.baf" % dd.get_sample_name(paired.tumor_data))
prep_file = bubbletree.prep_vrn_file(vrn_files[0]["vrn_file"], vrn_files[0]["variantcaller"],
work_dir, paired, AmberWriter)
utils.symlink_plus(prep_file, out_file)
pcf_file = out_file + ".pcf"
if not utils.file_exists(pcf_file):
with file_transaction(paired.tumor_data, pcf_file) as tx_out_file:
r_file = os.path.join(os.path.dirname(tx_out_file), "bafSegmentation.R")
with open(r_file, "w") as out_handle:
out_handle.write(_amber_seg_script)
cmd = "%s && %s --no-environ %s %s %s" % (utils.get_R_exports(), utils.Rscript_cmd(), r_file,
out_file, pcf_file)
do.run(cmd, "PURPLE: AMBER baf segmentation")
else:
assert method == "pon"
out_file = _run_amber(paired, work_dir)
return out_file
def _titan_het_file(vrn_files, work_dir, paired):
assert vrn_files, "Did not find compatible variant calling files for TitanCNA inputs"
from bcbio.heterogeneity import bubbletree
class OutWriter:
def __init__(self, out_handle):
self.writer = csv.writer(out_handle, dialect="excel-tab")
def write_header(self):
self.writer.writerow([
"Chr", "Position", "Ref", "RefCount", "Nref", "NrefCount",
"NormQuality"
])
def write_row(self, rec, stats):
if rec.qual and float(rec.qual) > 0:
self.writer.writerow([
rec.chrom, rec.pos, rec.ref,
stats["tumor"]["depth"] - stats["tumor"]["alt"],
rec.alts[0], stats["tumor"]["alt"], rec.qual
])
return bubbletree.prep_vrn_file(vrn_files[0]["vrn_file"],
vrn_files[0]["variantcaller"], work_dir,
paired, OutWriter)
def _amber_het_file(vrn_files, work_dir, paired):
"""Create file of BAFs in normal heterozygous positions compatible with AMBER.
https://github.com/hartwigmedical/hmftools/tree/master/amber
https://github.com/hartwigmedical/hmftools/blob/637e3db1a1a995f4daefe2d0a1511a5bdadbeb05/hmf-common/src/test/resources/amber/new.amber.baf
"""
assert vrn_files, "Did not find compatible variant calling files for TitanCNA inputs"
from bcbio.heterogeneity import bubbletree
prep_file = bubbletree.prep_vrn_file(vrn_files[0]["vrn_file"],
vrn_files[0]["variantcaller"],
work_dir, paired, AmberWriter)
amber_dir = utils.safe_makedir(os.path.join(work_dir, "amber"))
out_file = os.path.join(
amber_dir, "%s.amber.baf" % dd.get_sample_name(paired.tumor_data))
utils.symlink_plus(prep_file, out_file)
pcf_file = out_file + ".pcf"
if not utils.file_exists(pcf_file):
with file_transaction(paired.tumor_data, pcf_file) as tx_out_file:
r_file = os.path.join(os.path.dirname(tx_out_file),
"bafSegmentation.R")
with open(r_file, "w") as out_handle:
out_handle.write(_amber_seg_script)
cmd = "%s && %s --no-environ %s %s %s" % (utils.get_R_exports(
), utils.Rscript_cmd(), r_file, out_file, pcf_file)
do.run(cmd, "PURPLE: AMBER baf segmentation")
return out_file
def _amber_het_file(vrn_files, work_dir, paired):
"""Create file of BAFs in normal heterozygous positions compatible with AMBER.
https://github.com/hartwigmedical/hmftools/tree/master/amber
https://github.com/hartwigmedical/hmftools/blob/637e3db1a1a995f4daefe2d0a1511a5bdadbeb05/hmf-common/src/test/resources/amber/new.amber.baf
"""
assert vrn_files, "Did not find compatible variant calling files for TitanCNA inputs"
from bcbio.heterogeneity import bubbletree
prep_file = bubbletree.prep_vrn_file(vrn_files[0]["vrn_file"],
vrn_files[0]["variantcaller"],
work_dir, paired, OutWriter)
amber_dir = utils.safe_makedir(os.path.join(work_dir, "amber"))
out_file = os.path.join(
amber_dir, "%s.amber.baf" % dd.get_sample_name(paired.tumor_data))
utils.symlink_plus(prep_file, out_file)
return out_file
