korsair-api 1.1.5

We provide korsair-api to help you query and retrieve KORSAIR directly on your python code.

Korsair

Project description

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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

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Install with pip

python3 -m pip install korsair-api

Import korsair

from korsair_api import korsair

Functions

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• 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

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Gene Symbol: TP53 
Variant format: 7-140787574-C-T
dbSNP: rs397507456, Region: 17-7676272-7675994
Ensembl Gene: ENSG00000133703
Ensembl Transcript: ENST00000311936

1. get_variant

   korsair.get_vaiant('chr7', 140787574, 'C', 'T')
   

2. get_variant_id

   korsair.get_variant_id('rs397507456')
   

3. get_gene

   korsair.get_gene('CHD8')
   

4. get_region

   korsair.get_region(17, 7676272, 7675994)
   

5. extract_data(df, column, num)

   df = korsair.get_gene_('CHD8')
   extract_data(df, 'cadd_score', 20)
   

6. extract_none_rsid(df)

   df = korsair.get_gene_('CHD8')
   extract_none_rsid(df)
   

7. extract_filter(df, value)

   df = korsair.get_gene_('CHD8')
   extract_filter(df, 'pass')
   

Site

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KORSAIR