def main():
global options, args
separator = '|'
# Parse the HGVS name into genomic coordinates and alleles.
#chrom, offset, ref, alt = hgvs.parse_hgvs_name('ENST00000515609.1:c.30G>T', genome, get_transcript=get_transcript)
#print chrom, offset, ref, alt
# Format an HGVS name.
chrom, offset, ref, alt = ('chr2', 179616770, 'GAA', 'G')
transcript = get_transcript('ENST00000359218.5')
hgvs_name = hgvs.format_hgvs_name(chrom, offset, ref, alt, genome,
transcript)
print hgvs_name
chrom, offset, ref, alt = ('chr2', 179616770, 'GAA', 'GA')
transcript = get_transcript('ENST00000359218.5')
hgvs_name = hgvs.format_hgvs_name(chrom, offset, ref, alt, genome,
transcript)
hgvs_var = hgvs.HGVSName(hgvs_name)
hgvs_str = 'ENST00000359218.5:c.10597+1079_10597+1080delTTinsT'
hgvs_var2 = hgvs.HGVSName(hgvs_str)
print hgvs_name
quit()
# Open and parse each line of the vcf file
input_vcf = vcf.Reader(open(options.input_vcf, 'r'))
variant = Variant(samples=input_vcf.samples)
# Open output file
with open(options.output_vcf, 'w') as output_psv:
# Generate output file header
#variant = ConsequenceType(input_vcf.samples)
output_psv.write(variant.create_psv_header(separator=separator))
# Now parse lines in .vcf and output with new format:
for record in input_vcf:
# Only output sites that hasn't been filtered out
if len(record.FILTER) == 0:
#for consequence in range(0, len(record.INFO['CSQ'])):
variant.get_from_record(record=record)
output_psv.write(variant.put_to_psv(separator=separator))
def main():
global options, args
separator = '|'
# Parse the HGVS name into genomic coordinates and alleles.
#chrom, offset, ref, alt = hgvs.parse_hgvs_name('ENST00000515609.1:c.30G>T', genome, get_transcript=get_transcript)
#print chrom, offset, ref, alt
# Format an HGVS name.
chrom, offset, ref, alt = ('chr2', 179616770, 'GAA', 'G')
transcript = get_transcript('ENST00000359218.5')
hgvs_name = hgvs.format_hgvs_name(chrom, offset, ref, alt, genome, transcript)
print hgvs_name
chrom, offset, ref, alt = ('chr2', 179616770, 'GAA', 'GA')
transcript = get_transcript('ENST00000359218.5')
hgvs_name = hgvs.format_hgvs_name(chrom, offset, ref, alt, genome, transcript)
hgvs_var = hgvs.HGVSName(hgvs_name)
hgvs_str = 'ENST00000359218.5:c.10597+1079_10597+1080delTTinsT'
hgvs_var2 = hgvs.HGVSName(hgvs_str)
print hgvs_name
quit()
# Open and parse each line of the vcf file
input_vcf = vcf.Reader(open(options.input_vcf, 'r'))
variant = Variant(samples=input_vcf.samples)
# Open output file
with open(options.output_vcf, 'w') as output_psv:
# Generate output file header
#variant = ConsequenceType(input_vcf.samples)
output_psv.write(variant.create_psv_header(separator=separator))
# Now parse lines in .vcf and output with new format:
for record in input_vcf:
# Only output sites that hasn't been filtered out
if len(record.FILTER) == 0:
#for consequence in range(0, len(record.INFO['CSQ'])):
variant.get_from_record(record=record)
output_psv.write(variant.put_to_psv(separator=separator))
def vcf_to_hgvs(self, reference_transcript, vcf_notation):
"""
Converts a single VCF notation variant to HGVS notation relative to a given transcript.
@param reference_transcript: the refseq id of the reference transcript to use for HGVS notation
@type reference_transcript: string
@param vcf_notation: a tuple containing elements chromosome_number, coordinate, ref, and alt in that order
@type vcf_notation: tuple of strings
@return: hgvs notatation of variant in format reference_transcript:hgvs_description
@rtype: string
"""
chromosome_number, coordinate, ref, alt = vcf_notation
coordinate = int(coordinate)
transcript = self._get_transcript(reference_transcript)
return hgvs.format_hgvs_name(chromosome_number, coordinate, ref, alt, self.genome, transcript)
def vcf_to_hgvs(self, reference_transcript, vcf_notation):
"""
Converts a single VCF notation variant to HGVS notation relative to a given transcript.
See Counsyl's HGVS library for more information on acceptable input formats: https://github.com/counsyl/hgvs.
Args:
reference_transcript (str): the refseq id of the reference transcript to use for HGVS notation
vcf_notation (tuple of str): a tuple containing elements chromosome_number, coordinate, ref, and alt in that order
Returns:
str: hgvs notatation of variant in format reference_transcript:hgvs_description
"""
chromosome_number, coordinate, ref, alt = vcf_notation
coordinate = int(coordinate)
transcript = self._get_transcript(reference_transcript)
return hgvs.format_hgvs_name(chromosome_number, coordinate, ref, alt, self.genome, transcript)
return transcripts.get(name)
# Parse the HGVS name into genomic coordinates and alleles.
chrom, offset, ref, alt = hgvs.parse_hgvs_name(
'NM_000352.3:c.215A>G', genome, get_transcript=get_transcript)
print chrom, offset, ref, alt
# Returns variant in VCF style: ('chr11', 17496508, 'T', 'C')
# Notice that since the transcript is on the negative strand, the alleles
# are reverse complemented during conversion.
# Format an HGVS name.
chrom, offset, ref, alt = ('chr11', 17496508, 'T', 'C')
transcript = get_transcript('NM_000352.3')
hgvs_name = hgvs.format_hgvs_name(
chrom, offset, ref, alt, genome, transcript)
print hgvs_name
# Returns 'NM_000352.3(ABCC8):c.215A>G'
hgvs_name = hgvs.HGVSName('NM_000352.3:c.215-10A>G')
# fields of the HGVS name are available as attributes:
#
# hgvs_name.transcript = 'NM_000352.3'
# hgvs_name.kind = 'c'
# hgvs_name.mutation_type = '>'
# hgvs_name.cdna_start = hgvs.CDNACoord(215, -10)
# hgvs_name.cdna_end = hgvs.CDNACoord(215, -10)
# hgvs_name.ref_allele = 'A'
# hgvs_name.alt_allele = 'G'
return transcripts.get(name)
# Parse the HGVS name into genomic coordinates and alleles.
chrom, offset, ref, alt = hgvs.parse_hgvs_name('NM_000352.3:c.215A>G',
genome,
get_transcript=get_transcript)
print chrom, offset, ref, alt
# Returns variant in VCF style: ('chr11', 17496508, 'T', 'C')
# Notice that since the transcript is on the negative strand, the alleles
# are reverse complemented during conversion.
# Format an HGVS name.
chrom, offset, ref, alt = ('chr11', 17496508, 'T', 'C')
transcript = get_transcript('NM_000352.3')
hgvs_name = hgvs.format_hgvs_name(chrom, offset, ref, alt, genome, transcript)
print hgvs_name
# Returns 'NM_000352.3(ABCC8):c.215A>G'
hgvs_name = hgvs.HGVSName('NM_000352.3:c.215-10A>G')
# fields of the HGVS name are available as attributes:
#
# hgvs_name.transcript = 'NM_000352.3'
# hgvs_name.kind = 'c'
# hgvs_name.mutation_type = '>'
# hgvs_name.cdna_start = hgvs.CDNACoord(215, -10)
# hgvs_name.cdna_end = hgvs.CDNACoord(215, -10)
# hgvs_name.ref_allele = 'A'
# hgvs_name.alt_allele = 'G'
print(hgvs_name.transcript, hgvs_name.kind, hgvs_name.mutation_type,
