Genes#
The module genes provides functions related to Genes section of
cBioPortal Web Public API.
- pybioportal.genes.fetch_genes(gene_ids, gene_id_type='ENTREZ_GENE_ID', projection='SUMMARY')#
Fetch genes by Entrez Gene IDs or Hugo Gene Symbols.
- Parameters:
gene_ids (list of str) – List of Entrez Gene IDs or Hugo Gene Symbols (e.g., [“BRCA1”,”BRCA2”]).
gene_id_type (str) –
Type of gene ID.
Possible values:
”ENTREZ_GENE_ID” (default): Entrez Gene IDs.
”HUGO_GENE_SYMBOL”: Hugo Gene Symbols.
projection (str) –
Level of detail of the response.
Possible values:
”DETAILED”: Detailed information.
”ID”: Information with only IDs.
”META”: Metadata information.
”SUMMARY”: Summary information (default).
- Returns:
A DataFrame containing genes based on the specified Entrez Gene IDs or Hugo Gene Symbols.
- Return type:
pandas.DataFrame
- pybioportal.genes.get_aliases_of_gene(gene_id)#
Get aliases of a gene by Entrez Gene ID or Hugo Gene Symbol.
- Parameters:
gene_id (str) – Entrez Gene ID or Hugo Gene Symbol (e.g., “1” or “A1BG”).
- Returns:
A DataFrame containing aliases for the specified gene.
- Return type:
pandas.DataFrame
- pybioportal.genes.get_all_genes(alias=None, direction='ASC', keyword=None, pageNumber=0, pageSize=10000000, projection='SUMMARY', sortBy='hugoGeneSymbol')#
Get all genes based on filter criteria (alias or keyword).
- Parameters:
alias (str) – Alias of the gene.
direction (str) –
Direction of the sort.
Possible values:
”ASC”: Ascending (default)
”DESC”: Descending
keyword (str) – Search keyword that applies to hugo gene symbol of the genes.
pageNumber (int) –
Page number of the result list.
Minimum value is 0.
pageSize (int) –
Page size of the result list.
Minimum value is 1, maximum value is 10000000.
projection (str) –
Level of detail of the response.
Possible values:
”DETAILED”: Detailed information.
”ID”: Information with only IDs.
”META”: Metadata information.
”SUMMARY”: Summary information (default).
sortBy (str) –
Name of the property that the result list is sorted by.
Possible values:
”cytoband”
”entrezGeneId”
”hugoGeneSymbol” (default)
”length”
”type”
- Returns:
A DataFrame containing genes based on the specified filter criteria.
- Return type:
pandas.DataFrame
- pybioportal.genes.get_gene(gene_id)#
Get gene information by Entrez Gene ID or Hugo Gene Symbol.
- Parameters:
gene_id (str) – Entrez Gene ID or Hugo Gene Symbol (e.g., “1” or “A1BG”).
- Returns:
A DataFrame containing information about the specified gene.
- Return type:
pandas.DataFrame
Examples#
from pybioportal import genes as gns
df1a = gns.get_all_genes(keyword = "BRCA1")
df1a
| entrezGeneId | hugoGeneSymbol | type | |
|---|---|---|---|
| 0 | 394269 | BRCA1P1 | pseudogene |
| 1 | 672 | BRCA1 | protein-coding |
df1b = gns.get_all_genes(alias = "FANCS")
df1b
| entrezGeneId | hugoGeneSymbol | type | |
|---|---|---|---|
| 0 | 672 | BRCA1 | protein-coding |
df2 = gns.get_gene("BRCA1")
df2
| entrezGeneId | hugoGeneSymbol | type | |
|---|---|---|---|
| 0 | 672 | BRCA1 | protein-coding |
df3 = gns.get_aliases_of_gene("BRCA2")
df3
| 0 | |
|---|---|
| 0 | FAD1 |
| 1 | FANCD1 |
| 2 | XRCC11 |
df4 = gns.fetch_genes(gene_ids=["BRCA1","BRCA2"], gene_id_type = "HUGO_GENE_SYMBOL")
df4
| entrezGeneId | hugoGeneSymbol | type | |
|---|---|---|---|
| 0 | 672 | BRCA1 | protein-coding |
| 1 | 675 | BRCA2 | protein-coding |