def main(config_file, env, cores):
cores = int(cores)
config = read_config(config_file, env)
idremap = read_remap_file(config["runinfo"]["idmapping"])
exclude = read_priority_file(config["runinfo"]["priority"], idremap)
samples = list(get_input_samples(config["inputs"], idremap))
problem = [x for x in samples if x["id"] is None]
if len(problem) > 0:
print "Problem identifiers"
for p in problem:
print p["illuminaid"], os.path.basename(p["dir"])
raise NotImplementedError
check_fam(samples, config["runinfo"]["fam"])
config["algorithm"] = {"num_cores": cores}
samples = [
s for s in samples if s["id"] is not None and s["id"] not in exclude
]
print "Processing %s samples" % len(samples)
out_files = [
outf for outf in joblib.Parallel(cores)(
joblib.delayed(run_illumina_prep)(s, config) for s in samples)
]
merge_file = merge_vcf_files(out_files, cores, config)
effects_file = effects.snpeff_effects({
"vrn_file": merge_file,
"sam_ref": config["ref"]["GRCh37"],
"reference": {
"fasta": {
"base": config["ref"]["GRCh37"]
}
},
"genome_resources": {
"aliases": {
"snpeff": "GRCh37.74"
}
},
"genome_build": "GRCh37",
"config": config
})
data = {"config": config, "dirs": {"work": os.getcwd()}, "name": [""]}
gemini_db = population.prep_gemini_db(
[os.path.join(os.getcwd(), effects_file)],
[utils.splitext_plus(config["outputs"]["merge"])[0], "casava", True],
[{
"config": config,
"work_bam": "yes",
"genome_build": "GRCh37",
"genome_resources": {
"aliases": {
"human": True
}
}
}], data)[0][1]["db"]
print gemini_db
noexclude_file = "%s-noexclude%s" % utils.splitext_plus(effects_file)
noexclude_file = vcfutils.exclude_samples(effects_file, noexclude_file,
exclude, config["ref"]["GRCh37"],
config)
prepare_plink_vcftools(noexclude_file, config)
def main(config_file, env, cores):
cores = int(cores)
config = read_config(config_file, env)
idremap = read_remap_file(config["runinfo"]["idmapping"])
exclude = read_priority_file(config["runinfo"]["priority"], idremap)
samples = list(get_input_samples(config["inputs"], idremap))
problem = [x for x in samples if x["id"] is None]
if len(problem) > 0:
print "Problem identifiers"
for p in problem:
print p["illuminaid"], os.path.basename(p["dir"])
raise NotImplementedError
check_fam(samples, config["runinfo"]["fam"])
config["algorithm"] = {"num_cores": cores}
samples = [s for s in samples if s["id"] is not None and s["id"] not in exclude]
print "Processing %s samples" % len(samples)
out_files = [outf for outf in joblib.Parallel(cores)(joblib.delayed(run_illumina_prep)(s, config)
for s in samples)]
merge_file = merge_vcf_files(out_files, cores, config)
effects_file = effects.snpeff_effects({"vrn_file": merge_file,
"sam_ref": config["ref"]["GRCh37"],
"reference": {"fasta" : {"base": config["ref"]["GRCh37"]}},
"genome_resources": {"aliases" : {"snpeff": "GRCh37.74"}},
"genome_build": "GRCh37",
"config": config})
data = {"config": config, "dirs": {"work": os.getcwd()}, "name": [""]}
gemini_db = population.prep_gemini_db([os.path.join(os.getcwd(), effects_file)],
[utils.splitext_plus(config["outputs"]["merge"])[0], "casava", True],
[{"config": config, "work_bam": "yes", "genome_build": "GRCh37",
"genome_resources": {"aliases": {"human": True}}}],
data)[0][1]["db"]
print gemini_db
noexclude_file = "%s-noexclude%s" % utils.splitext_plus(effects_file)
noexclude_file = vcfutils.exclude_samples(effects_file, noexclude_file, exclude,
config["ref"]["GRCh37"], config)
prepare_plink_vcftools(noexclude_file, config)
def prep_gemini_db(*args):
return population.prep_gemini_db(*args)
def prep_gemini_db(*args):
return population.prep_gemini_db(*args)
