def get_coding_regions_for_gene(gene):
"""
Get list of sorted coding regions for gene
(assuming gene['cds'] contains raw cds vals
"""
cdr_list = []
# map of coordinate tuple -> cdr
cdrs = [(c['xstart'], c['xstop']) for c in gene['cds']]
flattened_cdrs = region_utils.flatten_region_list(cdrs)
for i, cdr_t in enumerate(flattened_cdrs):
cdr_list.append(CodingRegion(gene_id=gene['gene_id'], index_in_gene=i, xstart=cdr_t[0], xstop=cdr_t[1]))
return cdr_list
def get_coding_regions_from_gene_structure(gene_id, gene_structure):
"""
Get list of sorted coding regions for gene
(assuming gene['cds'] contains raw cds vals
"""
cdr_list = []
cdrs = [(c['cds_xstart'], c['cds_xstop']) for c in gene_structure['exons'] if 'cds_xstart' in c]
cdrs = sorted(cdrs, key=lambda x: (x[0], x[1]))
flattened_cdrs = region_utils.flatten_region_list(cdrs)
for i, cdr_t in enumerate(flattened_cdrs):
cdr_list.append(CodingRegion(gene_id=gene_id, index_in_gene=i, xstart=cdr_t[0], xstop=cdr_t[1]))
return cdr_list
def get_coding_regions_from_gene_structure(gene_id, gene_structure):
"""
Get list of sorted coding regions for gene
(assuming gene['cds'] contains raw cds vals
"""
cdr_list = []
cdrs = [(c['cds_xstart'], c['cds_xstop']) for c in gene_structure['exons']
if 'cds_xstart' in c]
cdrs = sorted(cdrs, key=lambda x: (x[0], x[1]))
flattened_cdrs = region_utils.flatten_region_list(cdrs)
for i, cdr_t in enumerate(flattened_cdrs):
cdr_list.append(
CodingRegion(gene_id=gene_id,
index_in_gene=i,
xstart=cdr_t[0],
xstop=cdr_t[1]))
return cdr_list