rnalysis.filtering.Filter.translate_gene_ids

Filter.translate_gene_ids(translate_to: str | Literal['UniProtKB AC/ID', 'UniParc', 'UniRef50', 'UniRef90', 'UniRef100', 'Gene Name', 'CRC64', 'Ensembl', 'Ensembl Genomes', 'Ensembl Genomes Protein', 'Ensembl Genomes Transcript', 'Ensembl Protein', 'Ensembl Transcript', 'GeneID', 'KEGG', 'PATRIC', 'UCSC', 'WBParaSite', 'WBParaSite Transcript/Protein', 'ArachnoServer', 'Araport', 'CGD', 'ConoServer', 'dictyBase', 'EchoBASE', 'euHCVdb', 'FlyBase', 'GeneCards', 'GeneReviews', 'HGNC', 'LegioList', 'Leproma', 'MaizeGDB', 'MGI', 'MIM', 'neXtProt', 'OpenTargets', 'Orphanet', 'PharmGKB', 'PomBase', 'PseudoCAP', 'RGD', 'SGD', 'TubercuList', 'VEuPathDB', 'VGNC', 'WormBase', 'WormBase Protein', 'WormBase Transcript', 'Xenbase', 'ZFIN', 'eggNOG', 'GeneTree', 'HOGENOM', 'OMA', 'OrthoDB', 'TreeFam', 'CCDS', 'EMBL/GenBank/DDBJ', 'EMBL/GenBank/DDBJ CDS', 'GI number', 'PIR', 'RefSeq Nucleotide', 'RefSeq Protein', 'ChiTaRS', 'GeneWiki', 'GenomeRNAi', 'PHI-base', 'CollecTF', 'BioCyc', 'PlantReactome', 'Reactome', 'UniPathway', 'CPTAC', 'ProteomicsDB'], translate_from: str | Literal['auto'] | Literal['UniProtKB AC/ID', 'UniParc', 'UniRef50', 'UniRef90', 'UniRef100', 'Gene Name', 'CRC64', 'Ensembl', 'Ensembl Genomes', 'Ensembl Genomes Protein', 'Ensembl Genomes Transcript', 'Ensembl Protein', 'Ensembl Transcript', 'GeneID', 'KEGG', 'PATRIC', 'UCSC', 'WBParaSite', 'WBParaSite Transcript/Protein', 'ArachnoServer', 'Araport', 'CGD', 'ConoServer', 'dictyBase', 'EchoBASE', 'euHCVdb', 'FlyBase', 'GeneCards', 'GeneReviews', 'HGNC', 'LegioList', 'Leproma', 'MaizeGDB', 'MGI', 'MIM', 'neXtProt', 'OpenTargets', 'Orphanet', 'PharmGKB', 'PomBase', 'PseudoCAP', 'RGD', 'SGD', 'TubercuList', 'VEuPathDB', 'VGNC', 'WormBase', 'WormBase Protein', 'WormBase Transcript', 'Xenbase', 'ZFIN', 'eggNOG', 'GeneTree', 'HOGENOM', 'OMA', 'OrthoDB', 'TreeFam', 'CCDS', 'EMBL/GenBank/DDBJ', 'EMBL/GenBank/DDBJ CDS', 'GI number', 'PIR', 'RefSeq Nucleotide', 'RefSeq Protein', 'ChiTaRS', 'GeneWiki', 'GenomeRNAi', 'PHI-base', 'CollecTF', 'BioCyc', 'PlantReactome', 'Reactome', 'UniPathway', 'CPTAC', 'ProteomicsDB'] = 'auto', remove_unmapped_genes: bool = False, inplace: bool = True)

Translates gene names/IDs from one type to another. Mapping is done using the UniProtKB Gene ID Mapping service. You can choose to optionally drop from the table all rows that failed to be translated.

Parameters:

  • translate_to (str) – the gene ID type to translate gene names/IDs to. For example: UniProtKB, Ensembl, Wormbase.

  • translate_from (str or 'auto' (default='auto')) – the gene ID type to translate gene names/IDs from. For example: UniProtKB, Ensembl, Wormbase. If translate_from=’auto’, RNAlysis will attempt to automatically determine the gene ID type of the features in the table.

  • remove_unmapped_genes (bool (default=False)) – if True, rows with gene names/IDs that could not be translated will be dropped from the table. Otherwise, they will remain in the table with their original gene name/ID.

  • inplace (bool (default=True)) – If True (default), filtering will be applied to the current Filter object. If False, the function will return a new Filter instance and the current instance will not be affected.

Returns:

If inplace is False, returns a new and translated instance of the Filter object.