lib5c.parsers.genes module¶
Module for parsing .bed files containing gene track information.
-
lib5c.parsers.genes.
load_gene_table
(tablefile)[source]¶ Similar to
load_genes()
, but reads in a gzipped UCSC table file instead.The main advantage of this approach is that genes parsed this way include human-readable gene symbols.
- Parameters
tablefile (str) – String reference to location of the gzipped table file to read.
- Returns
The keys are chromosome names. The values are lists of genes for that chromosome. The genes are represented as dicts with the following structure:
{ 'start' : int, 'end' : int, 'name' : str, 'id': str, 'strand': '+' or '-', 'blocks': list of dicts }
Blocks typically represent exons and are represented as dicts with the following structure:
{ 'start': int, 'end' : int }
- Return type
dict of lists of dicts
-
lib5c.parsers.genes.
load_genes
(bedfile)[source]¶ Loads information for genes from a .bed file into dicts and returns them.
- Parameters
bedfile (str) – String reference to location of .bed file to load genes from.
- Returns
The keys are chromosome names. The values are lists of genes for that chromosome. The genes are represented as dicts with the following structure:
{ 'start' : int, 'end' : int, 'name' : str, 'strand': '+' or '-', 'blocks': list of dicts }
Blocks typically represent exons and are represented as dicts with the following structure:
{ 'start': int, 'end' : int }
- Return type
dict of lists of dicts