We provide korsair-api to help you query and retrieve KORSAIR directly on your python code.
Project description
Korsair
Project description
korsair-api is a library package providing APIs to query the KORSAIR database(http://korsair.kisti.re.kr/), Korean Reference SNP and Indel Repository. We provide korsair-api to help you query and retrieve KORSAIR directly on your python code. With korsair-api, users can filter the query result based on the variant's information annotated with VEP, such as CADD score. korsair-api communicates with KORSAIR by REST APIs provided by KORSAIR.
Install and Import
Install with pip
python3 -m pip install korsair-api
Import korsair
from korsair_api import korsair
Functions
- get_variant(chro, pos, ref, alt)
- get_variant_id(rsid)
- get_gene(gene_id)
- get_region(chro, start, end)
- extract_data(df, column, num)
- extract_none_rsid(df)
- extract_filter(df, value)
Simple Example
Gene Symbol: TP53
Variant format: 7-140787574-C-T
dbSNP: rs397507456, Region: 17-7676272-7675994
Ensembl Gene: ENSG00000133703
Ensembl Transcript: ENST00000311936
-
get_variant
korsair.get_vaiant('chr7', 140787574, 'C', 'T')
-
get_variant_id
korsair.get_variant_id('rs397507456')
-
get_gene
korsair.get_gene('CHD8')
-
get_region
korsair.get_region(17, 7676272, 7675994)
-
extract_data(df, column, num)
df = korsair.get_gene_('CHD8') extract_data(df, 'cadd_score', 20)
-
extract_none_rsid(df)
df = korsair.get_gene_('CHD8') extract_none_rsid(df)
-
extract_filter(df, value)
df = korsair.get_gene_('CHD8') extract_filter(df, 'pass')
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