def main():
global options, args
separator = '|'
# Open and parse each line of the vcf file
input_vcf = vcf.Reader(open(options.input_vcf, 'r'))
if options.non_model:
variant = Variant(samples=input_vcf.samples,
organism_type='non_model',
ploidy=options.ploidy)
else:
variant = Variant(samples=input_vcf.samples, ploidy=options.ploidy)
# 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 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 = '|'
# Open and parse each line of the vcf file
input_vcf = vcf.Reader(open(options.input_vcf, 'r'))
if options.non_model:
variant = Variant(samples=input_vcf.samples, organism_type='non_model', ploidy=options.ploidy)
else:
variant = Variant(samples=input_vcf.samples, ploidy=options.ploidy)
# 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))
