Translation of homologs (gene.homology
)¶
This module is an interface to NCBI HomoloGene.
-
orangecontrib.bio.gene.homology.
all_genes
(taxid)¶ Return a set of all genes for organism taxid.
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orangecontrib.bio.gene.homology.
homologs
(genename, taxid)¶ Return a list of homologs (taxid, genename) for a homolog group of gene (organism taxid).
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orangecontrib.bio.gene.homology.
homolog
(genename, taxid, homolotaxid)¶ Return a homolog of genename (for taxid) in organism holomotaxid. If the homolog does not exist, return None.
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orangecontrib.bio.gene.homology.
orthologs
(genename, taxid, ortholog_taxid=None)¶ Return all InParanoid orthologs of genename from organism with taxid. If ortholog_taxid is given limit to orthologs from that organism only.
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orangecontrib.bio.gene.homology.
all_genes_inParanoid
(taxid)¶ Return a set of all genes for organism with taxid in the InParanoid database.
Examples¶
Mapping homologs from yeast to human:
import orangecontrib.bio.gene
import orangecontrib.bio.taxonomy
import Orange
data = Orange.data.Table("brown-selected")
geneinfo = orangecontrib.bio.gene.NCBIGeneInfo('4932')
genes = [str(ex["gene"]) for ex in data]
for gene in genes:
mappedgene = orangecontrib.bio.gene.homology.homolog(geneinfo(gene).symbol, \
'4932', '9606')
print(gene, mappedgene)