Getting Records¶
CIViCpy offeres a wide range of convenience methods as part of the civic module to retrieve different CIViC entities.
Get All Records For A Specific Entity Type¶
Features¶
Variants¶
Molecular Profiles¶
Assertions¶
Evidence Items¶
Variant Groups¶
Sources¶
Diseases¶
Therapies¶
Phenotypes¶
Organizations¶
Approvals
By ID¶
Records can be obtained by CIViC ID through a collection of functions provided in the civic module.
Features¶
Variants¶
Molecular Profiles¶
Assertions¶
Evidence Items¶
Variant Groups¶
Sources¶
Diseases¶
Therapies¶
Phenotypes¶
Organizations¶
Approvals¶
By Coordinates¶
Variant records can be searched by GRCh37 coordinates. To query specific genomic coordinates, you will
need to construct a CoordinateQuery object, and pass this query to the
search_variants_by_coordinates() function. If you wish to query multiple genomic coordinates (e.g.
a set of variants observed in a patient tumor), construct a sorted list of CoordinateQuery objects
(sorted by chr, start, stop, alt), and pass the list to the bulk_search_variants_by_coordinates()
function.
Coordinates can also be used to query Assertion and
Evidence records: