def annotate_mutation(self, mutation):
#if any([c in mutation for c in self.output_headers]):
for c in self.output_headers:
if c in mutation:
raise Exception(
'Error: Non-unique header value in annotation table (%s)' %
(c))
if all([mutation.chr, mutation.start, mutation.end]):
chrom, start, end = mutation.chr, mutation.start, mutation.end
records = get_binned_data(self.db_obj, chrom, int(start), int(end))
records = get_overlapping_records(records, int(start), int(end))
if records:
for c in self.output_headers:
summarized_results = get_summary_output_string(
[r[c].strip() for r in records])
mutation.createAnnotation(c,
summarized_results,
annotationSource=self.title)
for header in self.output_headers:
if header not in mutation:
mutation.createAnnotation(header,
'',
annotationSource=self.title)
return mutation
def annotate_mutation(self, mutation):
requiredAnnotations = ['gene', self.proteinPositionAnnotation]
if all(field in mutation for field in requiredAnnotations):
gene = mutation['gene']
p = None
transcriptProteinPos = []
proteinChange = mutation[self.proteinPositionAnnotation].replace("p.", "")
proteinPosition = self.proteinRegexp.match(proteinChange)
if proteinPosition is not None:
p = proteinPosition.group(1)
if p is not None:
records = get_binned_data(self.db_obj, gene, int(p), int(p))
records = get_overlapping_records(records, int(p), int(p))
for c in self.output_headers:
summarized_results = get_summary_output_string([r[c].strip() for r in records])
mutation.createAnnotation(c, summarized_results, annotationSource=self.title)
else:
missingList = []
for r in requiredAnnotations:
if r not in mutation:
missingList.append(r)
raise MissingAnnotationException("Missing required annotation: " + str(missingList))
for header in self.output_headers:
if header not in mutation:
mutation.createAnnotation(header, '', annotationSource=self.title)
return mutation
def annotate_mutation(self, mutation):
# if any([c in mutation for c in self.output_headers]):
for c in self.output_headers:
if c in mutation:
raise Exception("Error: Non-unique header value in annotation table (%s)" % (c))
if all(field in mutation for field in ["chr", "start", "end", "ref_allele", "alt_allele", "strand"]):
chr, start, end = mutation.chr, mutation.start, mutation.end
ref_allele, alt_allele = (
str(mutation.ref_allele),
str(mutation.alt_allele),
) # changed to str incase vcf.model._Substitution object is being used
if self.use_complementary_strand_alleles_for_negative_strand_transcripts:
if mutation.get("strand") == "-":
ref_allele, alt_allele = Seq.reverse_complement(ref_allele), Seq.reverse_complement(alt_allele)
records = get_binned_data(self.db_obj, chr, int(start), int(end))
records = get_overlapping_records(records, int(start), int(end))
records = [
rec
for rec in records
if rec[self.ref_allele_fieldname] == ref_allele and rec[self.alt_allele_fieldname] == alt_allele
]
if records:
for c in self.output_headers:
summarized_results = get_summary_output_string([r[c].strip() for r in records])
mutation.createAnnotation(c, summarized_results, annotationSource=self.title)
for header in self.output_headers:
if header not in mutation:
mutation.createAnnotation(header, "", annotationSource=self.title)
return mutation
def annotate_mutation(self, mutation):
requiredAnnotations = ['gene', self.proteinPositionAnnotation]
if all(field in mutation for field in requiredAnnotations):
gene = mutation['gene']
# p is a tuple (start, end)
p = None
transcriptProteinPos = []
proteinChange = mutation[self.proteinPositionAnnotation].replace(
"p.", "")
proteinPosition = self.protein_regex_range.match(proteinChange)
if proteinPosition is not None:
# Get start and end AA
p = (int(proteinPosition.group(1)),
int(proteinPosition.group(2)))
else:
# Get start and end AA as equal values, since this protein change can only have affected one AA, if any.
proteinPosition = self.protein_regexp.match(proteinChange)
if proteinPosition is not None:
p = (int(proteinPosition.group(1)),
int(proteinPosition.group(1)))
if p is not None:
records = get_binned_data(self.db_obj, gene, p[0], p[1])
records = get_overlapping_records(records, p[0], p[1])
for c in self.output_headers:
summarized_results = get_summary_output_string(
[r[c].strip() for r in records])
mutation.createAnnotation(c,
summarized_results,
annotationSource=self.title)
else:
missingList = []
for r in requiredAnnotations:
if r not in mutation:
missingList.append(r)
raise MissingAnnotationException("Missing required annotation: " +
str(missingList))
for header in self.output_headers:
if header not in mutation:
mutation.createAnnotation(header,
'',
annotationSource=self.title)
return mutation
def annotate_mutation(self, mutation):
requiredAnnotations = ['gene', self.proteinPositionAnnotation]
if all(field in mutation for field in requiredAnnotations):
gene = mutation['gene']
# p is a tuple (start, end)
p = None
transcriptProteinPos = []
proteinChange = mutation[self.proteinPositionAnnotation].replace("p.", "")
proteinPosition = self.protein_regex_range.match(proteinChange)
if proteinPosition is not None:
# Get start and end AA
p = (int(proteinPosition.group(1)), int(proteinPosition.group(2)))
else:
# Get start and end AA as equal values, since this protein change can only have affected one AA, if any.
proteinPosition = self.protein_regexp.match(proteinChange)
if proteinPosition is not None:
p = (int(proteinPosition.group(1)), int(proteinPosition.group(1)))
if p is not None:
records = get_binned_data(self.db_obj, gene, p[0], p[1])
records = get_overlapping_records(records, p[0], p[1])
for c in self.output_headers:
summarized_results = get_summary_output_string([r[c].strip() for r in records])
mutation.createAnnotation(c, summarized_results, annotationSource=self.title)
else:
missingList = []
for r in requiredAnnotations:
if r not in mutation:
missingList.append(r)
raise MissingAnnotationException("Missing required annotation: " + str(missingList))
for header in self.output_headers:
if header not in mutation:
mutation.createAnnotation(header, '', annotationSource=self.title)
return mutation
def annotate_mutation(self, mutation):
#if any([c in mutation for c in self.output_headers]):
for c in self.output_headers:
if c in mutation:
raise Exception('Error: Non-unique header value in annotation table (%s)' % (c))
if all([mutation.chr, mutation.start, mutation.end]):
chrom, start, end = mutation.chr, mutation.start, mutation.end
records = get_binned_data(self.db_obj, chrom, int(start), int(end))
records = get_overlapping_records(records, int(start), int(end))
if records:
for c in self.output_headers:
summarized_results = get_summary_output_string([r[c].strip() for r in records])
mutation.createAnnotation(c, summarized_results, annotationSource=self.title)
for header in self.output_headers:
if header not in mutation:
mutation.createAnnotation(header, '', annotationSource=self.title)
return mutation
def annotate_mutation(self, mutation):
#if any([c in mutation for c in self.output_headers]):
for c in self.output_headers:
if c in mutation:
raise Exception(
'Error: Non-unique header value in annotation table (%s)' %
(c))
if all(field in mutation for field in
['chr', 'start', 'end', 'ref_allele', 'alt_allele', 'strand']):
chr, start, end = mutation.chr, mutation.start, mutation.end
ref_allele, alt_allele = str(mutation.ref_allele), str(
mutation.alt_allele
) #changed to str incase vcf.model._Substitution object is being used
if self.use_complementary_strand_alleles_for_negative_strand_transcripts:
if mutation.get('strand') == '-':
ref_allele, alt_allele = Seq.reverse_complement(
ref_allele), Seq.reverse_complement(alt_allele)
records = get_binned_data(self.db_obj, chr, int(start), int(end))
records = get_overlapping_records(records, int(start), int(end))
records = [
rec for rec in records
if rec[self.ref_allele_fieldname] == ref_allele
and rec[self.alt_allele_fieldname] == alt_allele
]
if records:
for c in self.output_headers:
summarized_results = get_summary_output_string(
[r[c].strip() for r in records])
mutation.createAnnotation(c,
summarized_results,
annotationSource=self.title)
for header in self.output_headers:
if header not in mutation:
mutation.createAnnotation(header,
'',
annotationSource=self.title)
return mutation