def _compile_metaheaders(incoming_headers, vcf_readers, all_sample_names,
contigs_to_keep, format_tags_to_keep,
info_tags_to_keep):
#pylint: disable=too-many-arguments
ordered_metaheaders = list(incoming_headers)
all_info_metaheaders = {}
all_format_metaheaders = {}
all_contig_metaheaders = {}
for vcf_reader in vcf_readers:
all_info_metaheaders.update(vcf_reader.info_metaheaders)
all_format_metaheaders.update(vcf_reader.format_metaheaders)
all_contig_metaheaders.update(vcf_reader.contig_metaheaders)
all_info_metaheaders[_MULT_ALT_TAG] = _MULT_ALT_HEADER
if all_contig_metaheaders:
for contig_id in contigs_to_keep:
ordered_metaheaders.append(all_contig_metaheaders[contig_id])
for tag in info_tags_to_keep:
ordered_metaheaders.append(all_info_metaheaders[tag])
for tag in format_tags_to_keep:
ordered_metaheaders.append(all_format_metaheaders[tag])
sorted_metaheaders = utils.sort_metaheaders(ordered_metaheaders)
column_header = vcf_readers[0].column_header.split("\t")[0:9]
column_header.extend(all_sample_names)
sorted_metaheaders.append("\t".join(column_header))
return sorted_metaheaders
def _compile_metaheaders(incoming_headers,
vcf_readers,
all_sample_names,
contigs_to_keep,
format_tags_to_keep,
info_tags_to_keep):
#pylint: disable=too-many-arguments
ordered_metaheaders = list(incoming_headers)
all_info_metaheaders = {}
all_format_metaheaders = {}
all_contig_metaheaders = {}
for vcf_reader in vcf_readers:
all_info_metaheaders.update(vcf_reader.info_metaheaders)
all_format_metaheaders.update(vcf_reader.format_metaheaders)
all_contig_metaheaders.update(vcf_reader.contig_metaheaders)
all_info_metaheaders[_MULT_ALT_TAG] = _MULT_ALT_HEADER
if all_contig_metaheaders:
for contig_id in contigs_to_keep:
ordered_metaheaders.append(all_contig_metaheaders[contig_id])
for tag in info_tags_to_keep:
ordered_metaheaders.append(all_info_metaheaders[tag])
for tag in format_tags_to_keep:
ordered_metaheaders.append(all_format_metaheaders[tag])
sorted_metaheaders = utils.sort_metaheaders(ordered_metaheaders)
column_header = vcf_readers[0].column_header.split("\t")[0:9]
column_header.extend(all_sample_names)
sorted_metaheaders.append("\t".join(column_header))
return sorted_metaheaders
def test_sort_metaheaders_sortsWithinCategoryAlphaNum(self):
unsorted = [
"##contig=<ID=chr13", "##contig=<ID=chr1", "##contig=<ID=chr2"
]
actual = utils.sort_metaheaders(unsorted)
expected = [
"##contig=<ID=chr1", "##contig=<ID=chr2", "##contig=<ID=chr13"
]
self.assertEquals(expected, actual)
def _write_headers(reader, new_tags, execution_context, file_writer):
headers = reader.metaheaders
headers.extend(execution_context)
for tag in new_tags:
headers.append(tag.metaheader)
sorted_headers = utils.sort_metaheaders(headers)
sorted_headers.append(reader.column_header)
file_writer.write("\n".join(sorted_headers) + "\n")
def _write_headers(reader, new_tags, execution_context, file_writer):
headers = reader.metaheaders
headers.extend(execution_context)
for tag in new_tags:
headers.append(tag.metaheader)
sorted_headers = utils.sort_metaheaders(headers)
sorted_headers.append(reader.column_header)
file_writer.write("\n".join(sorted_headers) + "\n")
def test_sort_metaheaders_completeList(self):
unsorted = [
"##FORMAT", "##fileformat", "##INFO", "##jacquard.foo=", "##ALT",
"#CHROM", "##contig", "##FILTER"
]
actual = utils.sort_metaheaders(unsorted)
expected = [
"##fileformat", "##jacquard.foo=", "##contig", "##ALT", "##FILTER",
"##INFO", "##FORMAT", "#CHROM"
]
self.assertEquals(expected, actual)
def _write_metaheaders(caller,
vcf_reader,
file_writer,
execution_context=None,
new_meta_headers=None):
new_headers = list(vcf_reader.metaheaders)
if execution_context:
new_headers.extend(execution_context)
new_headers.extend(caller.get_metaheaders())
if new_meta_headers:
new_headers.append(new_meta_headers)
sorted_metaheaders = utils.sort_metaheaders(new_headers)
sorted_metaheaders.append(vcf_reader.column_header)
file_writer.write("\n".join(sorted_metaheaders) +"\n")
def _write_metaheaders(caller,
vcf_reader,
file_writer,
execution_context=None,
new_meta_headers=None):
new_headers = list(vcf_reader.metaheaders)
if execution_context:
new_headers.extend(execution_context)
new_headers.extend(caller.get_metaheaders())
if new_meta_headers:
new_headers.append(new_meta_headers)
sorted_metaheaders = utils.sort_metaheaders(new_headers)
sorted_metaheaders.append(vcf_reader.column_header)
file_writer.write("\n".join(sorted_metaheaders) + "\n")
def _write_zscores(caller, metaheaders, vcf_reader, file_writer):
#TODO: (jebene) make zscores and tmp file follow the same pattern when writing
try:
file_writer.open()
headers = list(metaheaders)
headers.extend(vcf_reader.metaheaders)
headers.extend(caller.metaheaders)
sorted_metaheaders = utils.sort_metaheaders(headers)
sorted_metaheaders.append(vcf_reader.column_header)
file_writer.write("\n".join(sorted_metaheaders) + "\n")
vcf_reader.open()
for vcf_record in vcf_reader.vcf_records():
line = caller.add_tags(vcf_record)
file_writer.write(line)
finally:
vcf_reader.close()
file_writer.close()
def _write_zscores(caller,
metaheaders,
vcf_reader,
file_writer):
#TODO: (jebene) make zscores and tmp file follow the same pattern when writing
try:
file_writer.open()
headers = list(metaheaders)
headers.extend(vcf_reader.metaheaders)
headers.extend(caller.metaheaders)
sorted_metaheaders = utils.sort_metaheaders(headers)
sorted_metaheaders.append(vcf_reader.column_header)
file_writer.write("\n".join(sorted_metaheaders) +"\n")
vcf_reader.open()
for vcf_record in vcf_reader.vcf_records():
line = caller.add_tags(vcf_record)
file_writer.write(line)
finally:
vcf_reader.close()
file_writer.close()
def test_sort_metaheaders_sortsWithinCategory(self):
unsorted = ["##FORMAT=DP", "##FORMAT=AF", "##jacquard.bar="]
actual = utils.sort_metaheaders(unsorted)
expected = ["##jacquard.bar=", "##FORMAT=AF", "##FORMAT=DP"]
self.assertEquals(expected, actual)
def test_sort_metaheaders_unexpectedMetaheadesr(self):
unsorted = ["##FORMAT", "##INFO", "##Strelka", "##MuTect", "##VarScan"]
actual = utils.sort_metaheaders(unsorted)
expected = ["##MuTect", "##Strelka", "##VarScan", "##INFO", "##FORMAT"]
self.assertEquals(expected, actual)
def test_sort_metaheaders_sortsWithinCategoryAlphaNum(self):
unsorted = ["##contig=<ID=chr13", "##contig=<ID=chr1", "##contig=<ID=chr2"]
actual = utils.sort_metaheaders(unsorted)
expected = ["##contig=<ID=chr1", "##contig=<ID=chr2", "##contig=<ID=chr13"]
self.assertEquals(expected, actual)
def test_sort_metaheaders_sortsWithinCategory(self):
unsorted = ["##FORMAT=DP", "##FORMAT=AF", "##jacquard.bar="]
actual = utils.sort_metaheaders(unsorted)
expected = ["##jacquard.bar=", "##FORMAT=AF", "##FORMAT=DP"]
self.assertEquals(expected, actual)
def test_sort_metaheaders_completeList(self):
unsorted = ["##FORMAT", "##fileformat", "##INFO", "##jacquard.foo=", "##ALT", "#CHROM", "##contig", "##FILTER"]
actual = utils.sort_metaheaders(unsorted)
expected = ["##fileformat", "##jacquard.foo=", "##contig", "##ALT", "##FILTER", "##INFO", "##FORMAT", "#CHROM"]
self.assertEquals(expected, actual)
def test_sort_metaheaders(self):
unsorted = ["##FORMAT", "##fileformat", "##INFO", "##jacquard.foo="]
actual = utils.sort_metaheaders(unsorted)
expected = ["##fileformat", "##jacquard.foo=", "##INFO", "##FORMAT"]
self.assertEquals(expected, actual)
def test_sort_metaheaders_unexpectedMetaheadesr(self):
unsorted = ["##FORMAT", "##INFO", "##Strelka", "##MuTect", "##VarScan"]
actual = utils.sort_metaheaders(unsorted)
expected = ["##MuTect", "##Strelka", "##VarScan", "##INFO", "##FORMAT"]
self.assertEquals(expected, actual)
def test_sort_metaheaders(self):
unsorted = ["##FORMAT", "##fileformat", "##INFO", "##jacquard.foo="]
actual = utils.sort_metaheaders(unsorted)
expected = ["##fileformat", "##jacquard.foo=", "##INFO", "##FORMAT"]
self.assertEquals(expected, actual)
