hgnc_queries.py

Query HGNC for gene symbols.
Created to attempt to rescue old gene symbols because of an old excel "database" that had to be converted in a Django database

Installation

pip install hgnc-queries

Examples:

Use HGNC queries to get:

>> import hgnc_queries
>> hgnc_queries.get_new_symbol("RN5S49", verbose = False)
RNA5SP49

>> hgnc_queries.get_gene_starting_with("BRCA", verbose = False)
["BRCA1", "BRCA1P1", "BRCA2", "BRCA3"]

>> hgnc_queries.get_alias("ARID1B", verbose = False)
["KIAA1235", "ELD/OSA1", "p250R", "BAF250b", "DAN15", "6A3-5"]

>> hgnc_queries.get_main_symbol(BRAF1, verbose = False)
BRAF

>> hgnc_queries.get_prev_symbol("COL2A1", verbose = False)
["SEDC", "AOM"]

>> hgnc_queries.get_id("BRAF", verbose = False)
HGNC:1097

>> hgnc_queries.get_symbol_from_id("1097", verbose = False)
BRAF

# new function more for in-script use
# get the hgnc symbol if gene symbol not recognized by the process you're using
>> print(queries.get_hgnc_symbol("RN5S49"))
RNA5SP49
>> print(queries.get_hgnc_symbol("BRAF1"))
BRAF

>> hgnc_queries.get_refseq("BRCA1", False)
['NM_007294']
>> hgnc_queries.get_ensembl("BRCA1", False)
"ENSG00000012048"

>> hgnc_queries.convert_refseq2ensembl("NM_007294", False)
"ENSG00000012048"
>> hgnc_queries.convert_ensembl2refseq("ENSG00000012048", False)
['NM_007294']