import os
from .get_gene_position import gene_position
from .gene_aliases import gene_aliases
[docs]def get_coordinates_genes(path: str = "", data_files: dict = {}):
"""
Get coordinates of all genes
Parameters
----------
path : str
data_files : dict
Returns
-------
essential_coordinates : dict
aliases_designation : dict
"""
essential_coordinates = {}
# Get position genes
if "gff3" in data_files:
file_path = os.path.join(path, data_files["gff3"])
gene_coordinates = gene_position(file_path)
else:
raise ValueError("gff3 type not found in data")
# Get all annotated essential genes
if "essential_genes" in data_files:
file_path = os.path.join(path, data_files["essentials"])
with open(file_path, "r") as f:
genes = f.readlines()[1:]
for gene in genes:
name = gene.strip("\n")
essential_coordinates[name] = gene_coordinates.get(name).copy()
else:
raise ValueError("essentials not found in data")
# Get aliases of all genes
if "gene_names" in data_files:
file_path = os.path.join(path, "Yeast_Protein_Names.txt")
aliases_designation = gene_aliases(file_path)[0] #'YMR056C' \ ['AAC1'], ...
else:
raise ValueError("gene_names not found in data")
return essential_coordinates, aliases_designation
