Parsing#
Additional parsing utilities, require pandas to be installed.
- class VariantSet(coordinates, alt_frequencies, preferred_ids, summary)#
Result of parsing with parse_dbsnp_variants().
- alt_frequencies#
Frequencies of the alternative alleles.
- coordinates#
Coordinates of the SNPs in the genome and consequence (e.g. intro_variant).
- preferred_ids#
Preferred identifiers map (old → new); old != new for merged variants.
- summary#
Data from DOCSUM field including GENE, HGVS, etc.
- parse_dbsnp_variants(snps_result, verbose=False)#
Parse coordinates, frequencies and preferred IDs of dbSNP variants.
- Parameters:
snps_result (
Union[EntrezResponse,Dict[tuple,EntrezResponse]]) – result of fetch query in XML format, usually to ‘snp’ databaseverbose (
bool) – whether to print out full problematic XML if SPDI cannot be parsed
- Return type:
- xml_to_string(element, indent=' ')#
Convert provided XML element to pretty indented string.
- Parameters:
element – the XML element to convert (data attribute of entrez result)
indent – the indentation to use, 4 spaces by default