uscbiostats / annoq-py

Python package for annoq-api-v2

This is a Python package for annoq-api-v2

Local Usage

Clone this repository

git clone https://github.com/USCbiostats/annoq-py.git

Install the package

pip install .

Open python on the terminal and import the package

python 
>>> from src.annoq import annoq

To run the tests

python -m pytest test/test.py

Get SNP by Chromosome Query

GetSNPsByChromosome(self, chr, start, end, fields, filter=None, page_from=None, page_size=None)

Returns list of json

Scrolling is done if page is more than 10k

Parameters

chr: str - Chromosome string

start: int - Start of chromosome

end: int - End of chromosome

fields: list[str] - List of strings with the fields that you

filter: list[str] (optional) - List of strings with fields that you want to filter on

page_from: int (optional) - Starting page number

page_size: int (optional) - Size of the page

annoq().get_SNPs_by_chromosome(chr="2", start=1, end=10000000, fields=['chr', 'ref', 'pos', 'rs_dbSNP151', 'ANNOVAR_ensembl_Effect', 'ANNOVAR_refseq_Effect'], query_type_option='SCROLL', filter=['chr'], page_from=2, page_size=4)

Get SNP by Gene Product Query

GetSNPsByGeneProduct(self, gene, fields, filter=None, page_from=None, page_size=None)

Returns list of json

Scrolling is done if page is more than 10k

Parameters

gene: str - Gene product string

fields: list[str] - List of strings with the fields that you

filter: list[str] (optional) - List of strings with fields that you want to filter on

page_from: int (optional) - Starting page number

page_size: int (optional) - Size of the page

annoq().get_SNPs_by_gene_product(gene="Q9BVC4", fields=["chr", "id"], filter=["chr", "pos"], page_from=0, page_size=10)

Get SNP by ID Query

GetSNPsByIDs(self, ids, fields, filter=None, page_from=None, page_size=None)

Returns list of json

Scrolling is done if page is more than 10k

Parameters

ids: list[str] - List of IDs

fields: list[str] - List of strings with the fields that you

filter: list[str] (optional) - List of strings with fields that you want to filter on

page_from: int (optional) - Starting page number

page_size: int (optional) - Size of the page

annoq().get_SNPs_by_IDs(ids=["2:10632C>A", "16:2255492G>A"], fields=["id", "chr"], query_type_option='SNPS', filter=["chr"], page_from=0, page_size=5)

Get SNP by RsID Query

GetSNPsByRsID(self, rsID, fields, filter=None, page_from=None, page_size=None)

Returns list of json

Scrolling is done if page is more than 10k

Parameters

rsID: str - rsID string

fields: list[str] - List of strings with the fields that you

filter: list[str] (optional) - List of strings with fields that you want to filter on

page_from: int (optional) - Starting page number

page_size: int (optional) - Size of the page

annoq().get_SNPs_by_RsID(rsID='rs189126619', fields=["rs_dbSNP151", "ref"], filter=["rs_dbSNP151"], page_from=0, page_size=2)

Get SNP by RsIDs Query

GetSNPsByRsIDs(self, rsIDs, fields, filter=None, page_from=None, page_size=None)

Returns list of json

Scrolling is done if page is more than 10k

Parameters

rsIDs: list[str] - list of rsIDs

fields: list[str] - List of strings with the fields that you

filter: list[str] (optional)- List of strings with fields that you want to filter on

page_from: int (optional) - Starting page number

page_size: int (optional) - Size of the page

annoq().get_SNPs_by_RsIDs(rsIDs=['rs189126619', 'rs115366554'], fields=["rs_dbSNP151", "ref"], query_type_option='SNPS', filter=["rs_dbSNP151"], page_from=0, page_size=2)

Count SNP by Chromosome Query

count_SNPs_by_chromosome(self, chr, start, end, filter)

return int

Parameters

chr: str - Chromosome string

start: int - Start of chromosome

end: int - End of chromosome

filter: list[str] (optional) - List of strings with fields that you want to filter on

annoq().count_SNPs_by_chromosome(chr="2", start=1, end=10000000, filter=["chr", "ANNOVAR_ensembl_Closest_gene(intergenic_only)"])

Count SNP by Gene Product Query

count_SNPs_by_gene_product(self, gene, filter)

return int

Parameters

gene: str - Gene product string

filter: list[str] (optional) - List of strings with fields that you want to filter on

annoq().count_SNPs_by_gene_product(gene="Q9BVC4", filter=["chr", "pos"])

Count SNP by ID Query

count_SNPs_by_IDs(self, ids, filter)

return int

Parameters

ids: list[str] - List of IDs

filter: list[str] (optional) - List of strings with fields that you want to filter on

annoq().count_SNPs_by_IDs(ids=["2:10632C>A", "2:10632C>A"], filter=["chr"])

Count SNP by RsID Query

count_SNPs_by_RsID(self, rsID, filter)

return int

Parameters

rsID: str - rsID string

filter: list[str] (optional) - List of strings with fields that you want to filter on

annoq().count_SNPs_by_RsID(rsID='rs189126619', filter=["rs_dbSNP151"])

Count SNP by RsIDs Query

count_SNPs_by_RsIDs(self, rsIDs, filter)

return int

Parameters

rsIDs: list[str] - list of rsIDs

filter: list[str] (optional) - List of strings with fields that you want to filter on

annoq().count_SNPs_by_RsIDs(rsIDs=['rs189126619', 'rs115366554'], filter=["rs_dbSNP151"])