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 # ********************** # store in DBNLVar # ********************** # Define connection parameters andd perform connection: connection = httplib2.Http(".cache") connection.add_credentials('*****@*****.**', 'prueba') # Open annotation file and parse each line in it annotation_vcf = vcf.Reader(open(options.input_vcf, 'r')) # Load metadata in variant object variant = Variant(samples=annotation_vcf.samples) for record in annotation_vcf: # Load variant information in DBNLVar, from consequences variant.get_from_record(record=record) for consequence in variant.consequences: resp = load_consequence(consequence=consequence) quit() # Store consequence non-relating data in DBNLVar if not check_record(table='chromosome', value=chrom_to_number(record.CHROM)): #payload = {'id': chrom_to_number(record.CHROM), 'name': number_to_chrom(chrom_to_number(record.CHROM))} load_record(payload=record) # Store consequence relating data in DBNLVar for consequence in record.INFO['CSQ']: for index, annotation in enumerate(consequence.split(separator)): payload = {} resp = requests.get(uri + 'chromosome/id/3/24.json', auth=auth) print resp.json() if resp.status_code == 200: content = resp.json()['content'] else: print "ERROR: Problem in query" raise print content
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 # ********************** # store in DBNLVar # ********************** # Define connection parameters andd perform connection: connection = httplib2.Http(".cache") connection.add_credentials("*****@*****.**", "prueba") # Open annotation file and parse each line in it annotation_vcf = vcf.Reader(open(options.input_vcf, "r")) # Load metadata in variant object variant = Variant(samples=annotation_vcf.samples) for record in annotation_vcf: # Load variant information in DBNLVar, from consequences variant.get_from_record(record=record) for consequence in variant.consequences: resp = load_consequence(consequence=consequence) quit() # Store consequence non-relating data in DBNLVar if not check_record(table="chromosome", value=chrom_to_number(record.CHROM)): # payload = {'id': chrom_to_number(record.CHROM), 'name': number_to_chrom(chrom_to_number(record.CHROM))} load_record(payload=record) # Store consequence relating data in DBNLVar for consequence in record.INFO["CSQ"]: for index, annotation in enumerate(consequence.split(separator)): payload = {} resp = requests.get(uri + "chromosome/id/3/24.json", auth=auth) print resp.json() if resp.status_code == 200: content = resp.json()["content"] else: print "ERROR: Problem in query" raise print content