def call_variant_varscan(bam, orig_genome_path, bed, conf):
pre_output = "varscan." + util.randstr() + ".mpileup"
vcfoutput = "output-vs." + util.randstr() + ".vcf"
bedarg = ""
if bed is not None:
bedarg = " -l " + bed
cmd = (
conf.get("main", "samtools_path")
+ " mpileup "
+ " -f "
+ orig_genome_path
+ " -o "
+ pre_output
+ " "
+ bedarg
+ " "
+ bam
)
subprocess.check_call(cmd, shell=True)
cmd2 = (
"java -Xmx2g -jar "
+ conf.get("main", "varscan_path")
+ " mpileup2cns "
+ pre_output
+ " --variants --output-vcf 1 --output-file "
+ vcfoutput
)
output = subprocess.check_output(cmd2, shell=True)
with open(vcfoutput, "w") as fh:
fh.write(output)
return util.bgz_tabix(vcfoutput, conf)
def normalize_nothing(orig_vcf, conf):
"""
Just copy the original vcf to a new, identical vcf file.
"""
new_vcf = util.strip_extensions(orig_vcf, ['vcf']) + '.nonorm.vcf'
cmd = 'cp {orig} {new}'.format(orig_vcf, new_ncf)
subprocess.check_call(cmd, shell=True)
return util.bgz_tabix(new_vcf, conf)
def compare_test_vcf(self, raw_orig_vcf, raw_test_vcf):
raw_orig_vcf = os.path.abspath(raw_orig_vcf)
raw_test_vcf = os.path.abspath(raw_test_vcf)
orig_vars = list(pysam.VariantFile(raw_orig_vcf))
tmp_dirname = util.strip_extensions(raw_test_vcf, ['gz','vcf']) + "-vcomp-" + util.randstr()
with util.TempDir(dirname=tmp_dirname):
orig_vcf = util.bgz_tabix(raw_orig_vcf, self.conf)
test_vcf = util.remove_halfcalls(raw_test_vcf)
test_vcf = util.bgz_tabix(test_vcf, self.conf)
caller_name = util.strip_extensions(test_vcf, ['gz','vcf'])
bed = util.vars_to_bed(orig_vars)
var_results = defaultdict(dict)
var_quals = self.collect_var_quals({caller_name: test_vcf}, bed, orig_vcf)
bamstats = defaultdict(dict)
for normalizer_name, normalizer in self.normalizers.iteritems():
logging.info("--> Running normalizer " + normalizer_name)
normed_orig_vcf = normalizer(orig_vcf, self.conf)
normed_caller_vcf = normalizer(test_vcf, self.conf)
for comparator_name, comparator in self.comparators.iteritems():
logging.info("--> Running comparator " + comparator_name + " (normalizer " + normalizer_name + ")")
all_results = comparator(normed_orig_vcf, normed_caller_vcf, None, self.conf)
single_results = split_results(all_results, bed)
for region, result in zip(util.read_regions(bed), single_results):
match_vars = util.find_matching_var(orig_vcf, region)
if not match_vars:
raise ValueError('Unable to find original variant from region ' + str(region))
result = compare_single_var(result,
region,
normed_orig_vcf,
normed_caller_vcf,
comparator,
"/".join(str(i) for i in match_vars[0].samples[0]['GT']),
self.conf)
key = var_key(match_vars)
if caller_name not in var_results[key]:
var_results[key][caller_name] = defaultdict(dict)
var_results[key][caller_name][normalizer_name][comparator_name] = result
bamstats[key] = {}
# Iterate over all results and write to standard output. We do this here instead of within the loops above
# because it keeps results organized by variant, which makes them easier to look at
self.reporter.write_output(var_results, var_quals, bamstats)
def normalize_vt(orig_vcf, conf):
"""
Use vt to normalize
:param conf: configuration object with path to reference genome and vt binary
:return: String describing variant matching result
"""
norm_orig_vcf = orig_vcf.replace(".vcf", ".norm.vt.vcf")
norm_orig_cmd = conf.get('main', 'vt') + " normalize " + " -r " + conf.get('main', 'ref_genome') + " " + orig_vcf + " -o " + norm_orig_vcf
subprocess.check_call(norm_orig_cmd.split(), stderr=open("/dev/null"))
return util.bgz_tabix(norm_orig_vcf, conf)
def normalize_nothing(orig_vcf, conf):
"""
Just copy the original vcf to a new, identical vcf file.
"""
newvcf_name = orig_vcf.replace(".vcf", ".nonorm.vcf")
cmd = "cp " + orig_vcf + " " + newvcf_name
subprocess.check_call(cmd, shell=True)
newvcf_name = util.bgz_tabix(newvcf_name, conf)
return newvcf_name
def normalize_bcftools(orig_vcf, conf):
"""
Use bcftools to normalize.
:param orig_vcf:
:param conf:
:return:
"""
norm_orig_vcf = orig_vcf.replace(".vcf.gz", ".norm.bcftools" + util.randstr() + ".vcf")
norm_orig_cmd = conf.get('main', 'bcftools') + " norm " + " -c w -f " + conf.get('main', 'ref_genome') + " " + orig_vcf + " -o " + norm_orig_vcf
subprocess.check_call(norm_orig_cmd.split())
return util.bgz_tabix(norm_orig_vcf, conf)
def call_variant_mp_bcf(bam, genome, bed, conf):
pre_output = "mpileup." + util.randstr() + ".vcf"
vcfoutput = "output-mp." + util.randstr() + ".vcf"
bedarg = ""
if bed is not None:
bedarg = " -l " + bed
cmd = conf.get('main','samtools') + ' mpileup ' + ' -f ' + genome + " -uv " + " -o " + pre_output + " " + bedarg + " " + bam
subprocess.check_call(cmd)
cmd2 = conf.get('main', 'bcftools') + ' call ' + ' -mv ' + ' -o ' + vcfoutput + " " + pre_output
subprocess.check_call(cmd2)
return util.bgz_tabix(vcfoutput, conf)
def call_variant_varscan_emit_all(bam, genome, bed, conf):
pre_output = "varscan." + util.randstr() + ".mpileup"
vcfoutput = "output-vs." + util.randstr() + ".vcf"
bedarg = ""
if bed is not None:
bedarg = " -l " + bed
cmd = conf.get('main','samtools') + ' mpileup ' + ' -f ' + genome + " -o " + pre_output + " " + bedarg + " " + bam
subprocess.check_call(cmd)
cmd2 = "java -Xmx2g -jar " + conf.get('main', 'varscan') + ' mpileup2cns ' + pre_output + ' --p-value 0.5 --variants --output-vcf 1 --output-file ' + vcfoutput
subprocess.check_call(cmd2, stdout=open(vcfoutput, 'w'))
return util.bgz_tabix(vcfoutput, conf)
def normalize_vap_leftalign(orig_vcf, conf):
orig_vcf = util.sort_vcf(orig_vcf, conf)
tmp_vcf = orig_vcf.replace(".vcf", ".vap.tmp.vcf").replace(".gz", "")
final_vcf = orig_vcf.replace(".vcf", ".vap.leftaligned.vcf")
norm_orig_cmd = conf.get('main', 'vcfallelicprimitives') + " " + orig_vcf
subprocess.check_call(norm_orig_cmd, shell=True, stdout=file(tmp_vcf, 'w'))
no_et = ""
try:
no_et = " -et NO_ET -K " + conf.get('main', 'gatk_no_et')
except:
pass
cmd = "java -Djava.io.tmpdir=. -Xmx1g -jar " + conf.get('main', 'gatk') + " -T LeftAlignAndTrimVariants " + no_et + " -R " + conf.get('main', 'ref_genome') + " -U ALLOW_SEQ_DICT_INCOMPATIBILITY -V " + tmp_vcf + " -o " + final_vcf
subprocess.check_call(cmd, shell=True)
return util.bgz_tabix(final_vcf, conf)
def normalize_vap_leftalign(orig_vcf, conf):
err = open("/dev/null")
orig_vcf = util.sort_vcf(orig_vcf, conf)
tmp_vcf = orig_vcf.replace(".vcf", ".vap.tmp.vcf").replace(".gz", "")
final_vcf = orig_vcf.replace(".vcf", ".vap.leftaligned.vcf")
norm_orig_cmd = conf.get('main', 'vcfallelicprimitives_path') + " " + orig_vcf
tmp_output=subprocess.check_output(norm_orig_cmd, shell=True)
with open(tmp_vcf, "w") as fh:
fh.write(tmp_output)
no_et = ""
try:
no_et = " -et NO_ET -K " + conf.get('main', 'gatk_no_et')
except:
pass
cmd = "java -Djava.io.tmpdir=. -Xmx1g -jar " + conf.get('main', 'gatk_path') + " -T LeftAlignAndTrimVariants " + no_et + " -R " + conf.get('main', 'ref_genome') + " -V " + tmp_vcf + " -o " + final_vcf
subprocess.check_output(cmd, shell=True)
err.close()
return util.bgz_tabix(final_vcf, conf)
def call_variant_mp_bcf(bam, orig_genome_path, bed, conf):
pre_output = "mpileup." + util.randstr() + ".vcf"
vcfoutput = "output-mp." + util.randstr() + ".vcf"
bedarg = ""
if bed is not None:
bedarg = " -l " + bed
cmd = (
conf.get("main", "samtools_path")
+ " mpileup "
+ " -f "
+ orig_genome_path
+ " -uv "
+ " -o "
+ pre_output
+ " "
+ bedarg
+ " "
+ bam
)
subprocess.check_call(cmd, shell=True)
cmd2 = conf.get("main", "bcftools_path") + " call " + " -mv " + " -o " + vcfoutput + " " + pre_output
subprocess.check_call(cmd2, shell=True)
return util.bgz_tabix(vcfoutput, conf)
