sincei.RegionQuery module

sincei.RegionQuery.get_gtf_adata_olaps(adata, gtf)

Get overlaps between AnnData features and GTF regions.

Parameters

adataAnnData

AnnData with regions to overlap.

gtfGTF

GTF object with regions to overlap.

Returns

dict

Dictionary with overlaps for each feature in adata.

Examples

>>> test = Tester()
>>> gtf = GTF(test.gtfFile)
>>> adata = sc.read_10x_mtx(test.input_matrix_dir, var_names='gene_symbols', cache=True)
>>> olaps=get_gtf_adata_olaps(adata, gtf)
>>> olaps['Gm37381']
[('ENSMUSG00000064372', '+'), ('ENSMUSG00000064372', '-')]

sincei.RegionQuery.get_bins_by_gene(dict, gene, firstBin=False)

Returns the bins for a given gene.

Parameters

dictdict

Dictionary of bins and genes.

genestr

Gene name.

firstBinbool

If true, return only the first bin of the gene.

Returns

list

List of bins.

Examples

>>> dict = {'chr1_1': [('gene1', '+'), ('gene2', '-')], 'chr1_2': [('gene1', '+')]}
>>> get_bins_by_gene(dict, 'gene1')
['chr1_1', 'chr1_2']
>>> get_bins_by_gene(dict, 'gene1', firstBin=True)
'chr1_1'