def vcf_summary(self):
if not self._check_pargs(["project"]):
return
flist = find_samples(os.path.abspath(os.path.join(self.app.controller._meta.project_root, self.app.controller._meta.path_id)), **vars(self.pargs))
vcf_d = get_vcf_files(flist, **vars(self.pargs))
## Traverse files, copy to result directory, run bgzip and tabix, and merge vcfs to one file
outdir = os.path.join(os.path.abspath(os.path.join(self.app.controller._meta.project_root, self.app.controller._meta.path_id, "intermediate", "results", "vcf")))
if not os.path.exists(outdir):
self.app.cmd.safe_makedir(outdir)
for k, v in vcf_d.iteritems():
# FIXME: this should be memoized
if os.path.exists("{}.tbi".format(v)):
self.app.log.info("{}.tbi exists; skipping bgzip and tabix operations".format(v))
continue
if not v.endswith(".gz"):
## bgzip
self.app.log.info("Running bgzip on {}".format(v))
cl = ["bgzip", v]
self.app.cmd.command(cl)
# tabix
self.app.log.info("Running tabix on {}.gz".format(v))
cl = ["tabix", "-f", "-p", "vcf", "{}.gz".format(v)]
self.app.cmd.command(cl)
# Make all-variants file
all_variants = os.path.join(outdir, "all-variants.vcf")
cl = ['vcf-merge'] + vcf_d.values()# + [">", all_variants]
if not os.path.exists(all_variants):
self.app.log.info("Merging vcf files {} to {}".format(vcf_d.values() ,all_variants))
output = self.app.cmd.command(cl)
with open(all_variants, "w") as fh:
fh.write(output)
cl = ['bgzip', all_variants]
self.app.cmd.command(cl)
cl = ['tabix', "-f", "-p", "vcf", "{}.gz".format(all_variants)]
self.app.cmd.command(cl)
def vcf_summary(self):
if not self._check_pargs(["project"]):
return
flist = find_samples(
os.path.abspath(
os.path.join(self.app.controller._meta.project_root,
self.app.controller._meta.path_id)),
**vars(self.pargs))
vcf_d = get_vcf_files(flist, **vars(self.pargs))
## Traverse files, copy to result directory, run bgzip and tabix, and merge vcfs to one file
outdir = os.path.join(
os.path.abspath(
os.path.join(self.app.controller._meta.project_root,
self.app.controller._meta.path_id, "intermediate",
"results", "vcf")))
vcf_out = []
if not os.path.exists(outdir):
self.app.cmd.safe_makedir(outdir)
for k, v in vcf_d.iteritems():
# FIXME: this should be memoized
if os.path.exists("{}.tbi".format(v)):
self.app.log.info(
"{}.tbi exists; skipping bgzip and tabix operations".
format(v))
vcf_out.append(v)
continue
if not v.endswith(".gz"):
## bgzip
self.app.log.info("Running bgzip on {}".format(v))
cl = ["bgzip", v]
self.app.cmd.command(cl)
vcf_out.append("{}.gz".format(v))
else:
vcf_out.append(v)
# tabix
self.app.log.info("Running tabix on {}.gz".format(v))
cl = ["tabix", "-f", "-p", "vcf", "{}.gz".format(v)]
self.app.cmd.command(cl)
# Make all-variants file
all_variants = os.path.join(outdir, "all-variants.vcf")
cl = ['vcf-merge'] + vcf_out
if not os.path.exists(all_variants):
self.app.log.debug("Merging vcf files {} to {}".format(
vcf_out, all_variants))
self.app.log.info("Merging {} vcf files to {}".format(
len(vcf_out), all_variants))
output = self.app.cmd.command(cl)
with open(all_variants, "w") as fh:
fh.write(output)
cl = ['bgzip', all_variants]
self.app.cmd.command(cl)
cl = ['tabix', "-f", "-p", "vcf", "{}.gz".format(all_variants)]
self.app.cmd.command(cl)
def vcf_summary(self):
if not self._check_pargs(["project"]):
return
flist = find_samples(
os.path.abspath(os.path.join(self.app.controller._meta.project_root, self.app.controller._meta.path_id)),
**vars(self.pargs)
)
vcf_d = get_vcf_files(flist)
## Traverse files, copy to result directory, run bgzip and tabix, and merge vcfs to one file
outdir = os.path.join(
os.path.abspath(
os.path.join(
self.app.controller._meta.project_root,
self.app.controller._meta.path_id,
"intermediate",
"results",
"vcf",
)
)
)
if not os.path.exists(outdir):
self.app.cmd.safe_makedir(outdir)
for k, v in vcf_d.iteritems():
print v
if v.endswith(".gz"):
tgt = os.path.join(outdir, os.path.basename(v).replace("TOTAL", "TOTAL_{}".format(k)))
v = v.replace(".gz", "")
tgt = tgt.replace(".gz", "")
else:
## bgzip
LOG.info("Running bgzip on {}".format(v))
cl = ["bgzip", v]
self.app.cmd.command(cl)
##if not os.path.exists("{}.gz.tbi"):
## tabix
LOG.info("Running tabix on {}.gz".format(v))
cl = ["tabix", "-f", "-p", "vcf", "{}.gz".format(v)]
self.app.cmd.command(cl)
self.app.cmd.link("{}.gz".format(v), "{}.gz".format(tgt))
self.app.cmd.link("{}.gz.tbi".format(v), "{}.gz.tbi".format(tgt))
def test_summarize_variants(self):
"""Test summarizing variants"""
flist = find_samples(j_doe_00_01)
vcf_d = get_vcf_files(flist)
def test_summarize_variants(self):
"""Test summarizing variants"""
flist = find_samples(j_doe_00_01)
vcf_d = get_vcf_files(flist)
