def merge_perchrom_vcfs(job, perchrom_vcfs, tool_name, univ_options):
"""
Merge per-chromosome vcf files into a single genome level vcf.
:param dict perchrom_vcfs: Dictionary with chromosome name as key and fsID of the corresponding
vcf as value
:param str tool_name: Name of the tool that generated the vcfs
:returns: fsID for the merged vcf
:rtype: toil.fileStore.FileID
"""
work_dir = os.getcwd()
input_files = {
''.join([chrom, '.vcf']): jsid
for chrom, jsid in perchrom_vcfs.items()
}
input_files = get_files_from_filestore(job,
input_files,
work_dir,
docker=False)
first = True
with open(''.join([work_dir, '/', 'all_merged.vcf']), 'w') as outvcf:
for chromvcfname in chrom_sorted(
[x.rstrip('.vcf') for x in input_files.keys()]):
with open(input_files[chromvcfname + '.vcf'], 'r') as infile:
for line in infile:
line = line.strip()
if line.startswith('#'):
if first:
print(line, file=outvcf)
continue
first = False
print(line, file=outvcf)
output_file = job.fileStore.writeGlobalFile(outvcf.name)
export_results(job,
output_file,
outvcf.name,
univ_options,
subfolder='mutations/' + tool_name)
job.fileStore.logToMaster('Ran merge_perchrom_vcfs for %s successfully' %
tool_name)
return output_file
def merge_perchrom_mutations(job, chrom, mutations, univ_options):
"""
Merge the mutation calls for a single chromosome.
:param str chrom: Chromosome to process
:param dict mutations: dict of dicts of the various mutation caller names as keys, and a dict of
per chromosome job store ids for vcfs as value
:param dict univ_options: Dict of universal options used by almost all tools
:returns fsID for vcf contaning merged calls for the given chromosome
:rtype: toil.fileStore.FileID
"""
work_dir = os.getcwd()
from protect.mutation_calling.muse import process_muse_vcf
from protect.mutation_calling.mutect import process_mutect_vcf
from protect.mutation_calling.radia import process_radia_vcf
from protect.mutation_calling.somaticsniper import process_somaticsniper_vcf
from protect.mutation_calling.strelka import process_strelka_vcf
mutations.pop('indels')
mutations['strelka_indels'] = mutations['strelka']['indels']
mutations['strelka_snvs'] = mutations['strelka']['snvs']
vcf_processor = {
'snvs': {
'mutect': process_mutect_vcf,
'muse': process_muse_vcf,
'radia': process_radia_vcf,
'somaticsniper': process_somaticsniper_vcf,
'strelka_snvs': process_strelka_vcf
},
'indels': {
'strelka_indels': process_strelka_vcf
}
}
# 'fusions': lambda x: None,
# 'indels': lambda x: None}
# For now, let's just say 2 out of n need to call it.
# num_preds = len(mutations)
# majority = int((num_preds + 0.5) / 2)
majority = {'snvs': 2, 'indels': 1}
accepted_hits = defaultdict(dict)
for mut_type in vcf_processor.keys():
# Get input files
perchrom_mutations = {
caller:
vcf_processor[mut_type][caller](job, mutations[caller][chrom],
work_dir, univ_options)
for caller in vcf_processor[mut_type]
}
# Process the strelka key
perchrom_mutations['strelka'] = perchrom_mutations['strelka_' +
mut_type]
perchrom_mutations.pop('strelka_' + mut_type)
# Read in each file to a dict
vcf_lists = {
caller: read_vcf(vcf_file)
for caller, vcf_file in perchrom_mutations.items()
}
all_positions = list(set(itertools.chain(*vcf_lists.values())))
for position in sorted(all_positions):
hits = {
caller: position in vcf_lists[caller]
for caller in perchrom_mutations.keys()
}
if sum(hits.values()) >= majority[mut_type]:
callers = ','.join(
[caller for caller, hit in hits.items() if hit])
assert position[1] not in accepted_hits[position[0]]
accepted_hits[position[0]][position[1]] = (position[2],
position[3],
callers)
with open(''.join([work_dir, '/', chrom, '.vcf']), 'w') as outfile:
print('##fileformat=VCFv4.0', file=outfile)
print(
'##INFO=<ID=callers,Number=.,Type=String,Description=List of supporting callers.',
file=outfile)
print('#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO', file=outfile)
for chrom in chrom_sorted(accepted_hits.keys()):
for position in sorted(accepted_hits[chrom]):
print(chrom,
position,
'.',
accepted_hits[chrom][position][0],
accepted_hits[chrom][position][1],
'.',
'PASS',
'callers=' + accepted_hits[chrom][position][2],
sep='\t',
file=outfile)
fsid = job.fileStore.writeGlobalFile(outfile.name)
export_results(job,
fsid,
outfile.name,
univ_options,
subfolder='mutations/merged')
return fsid