module: genome_integration.gene_regions¶

These functions are being used to prioritize genes in certain already associated regions.

class genome_integration.gene_regions.StartEndRegion(*args, **kwargs)¶

Class that implements a genomic region, which is really a stretch of base pairs.

position_in_region(self, chr, position):: returns a bool on if the single position is within the region.
snp_in_region(chr, position): returns a bool on if the single position is within the region. synonym method of position in region.
snp_object_in_region(snp_object): returns a bool on if the object of class SNP is within the region.
region_overlaps(other_region): returns a bool if another of region of the same class overlaps.

position_in_region(chr, position)¶

return if the position is in the region.

Parameters:	chr – chromosome str or castable to str position – position int or castable to int
Returns:	bool

snp_in_region(chr, position)¶

return if the position is in the region. synonym method of position_in_region method.

Parameters:	chr – chromosome str or castable to str position – position int or castable to int
Returns:	bool

snp_object_in_region(snp_object)¶

Parameters:	snp_object – object of type SNP (this package)
Returns:	True or false if snp in region

class genome_integration.gene_regions.StartEndRegions(list_of_regions)¶

This class contains multiple start end regions

gene_regions: list of StartEndRegion objects

in_gene_regions(self, chr, position): identifies if a position is in any of the regions.
make_non_overlapping_regions(self): combines the regions into contiguous non-overlapping regions.

in_gene_regions(chr, position)¶

Identify if a snp is in any of the gene regions.

Parameters:	chr – chromosome castable to str position – position castable to int
Returns:	boolean

make_non_overlapping_regions()¶

Combines all overlapping regions, and turns them into one big region.

Returns:	new instance of StartEndRegions containing contiguous, non overlapping regions