Examples¶
Usage¶
For the most simple usage, use API which will get the latest mouse and human and map gene IDs to gene names.
Examples¶
from scibiomart import SciBiomartApi
sb = SciBiomartApi()
# Get only the default for those genes
results_df = sb.get_mouse_default({'ensembl_gene_id': 'ENSMUSG00000029844,ENSMUSG00000032446'})
# Select attributes
results_df = sb.get_mouse_default({'ensembl_gene_id': 'ENSMUSG00000020875,ENSMUSG00000038210'},
attr_list=['entrezgene_id'])
# Get all genes
results_df = sb.get_mouse_default()
# Sort the results based on TSS (takes direction into account)
results_df = sb.sort_df_on_starts(results_df)
# Get human
results_df = sb.get_human_default()
Examples extended¶
If you are interested in more than the simple API, see the tests for all examples, however, you can list the datasets etc, and query other attributes.
Print marts¶
sb = SciBiomart()
marts = sb.list_marts()
print('\n'.join(marts))
Print datasets¶
sb = SciBiomart()
sb.set_mart('ENSEMBL_MART_ENSEMBL')
err = sb.list_datasets()
List attributes¶
sb = SciBiomart()
sb.set_mart('ENSEMBL_MART_ENSEMBL')
sb.set_dataset('fcatus_gene_ensembl')
err = sb.list_attributes()
List configs¶
sb = SciBiomart()
sb.set_mart('ENSEMBL_MART_ENSEMBL')
sb.set_dataset('fcatus_gene_ensembl')
err = sb.list_configs()
List filters¶
sb = SciBiomart()
sb.set_mart('ENSEMBL_MART_ENSEMBL')
sb.set_dataset('fcatus_gene_ensembl')
err = sb.list_filters()
Run generic query¶
Here we show a generic query for two genes (as a comma separated list) and the attributes we’re interested in are ‘ensembl_gene_id’, ‘hgnc_symbol’, ‘uniprotswissprot’.
Run query: def run_query(self, filter_dict: dict, attr_list: list):
i.e. you can pass it a filter dictionary and a list of attributes. This will make it quicker, you can also run it and it
will get all genes (i.e. if filter_dict is empty).
sb = SciBiomart()
sb.set_mart('ENSEMBL_MART_ENSEMBL')
sb.set_dataset('hsapiens_gene_ensembl')
results = sb.run_query({'ensembl_gene_id': 'ENSG00000139618,ENSG00000091483'},
['ensembl_gene_id', 'hgnc_symbol', 'uniprotswissprot'])
print(results)
Match mouse to human¶
Get mouse orthologs for human genes
sb = SciBiomart()
sb.set_mart('ENSEMBL_MART_ENSEMBL')
sb.set_dataset('hsapiens_gene_ensembl')
attributes = ['ensembl_gene_id', 'mmusculus_homolog_ensembl_gene', 'mmusculus_homolog_perc_id_r1']
results = sb.run_query({'ensembl_gene_id': 'ENSG00000139618,ENSG00000091483'}, attributes)
print(results)
See tests for more examples