from transposonmapper.properties.get_gene_position import gene_position
from transposonmapper.properties.gene_aliases import gene_aliases
[docs]def read_genes(gff_file, essentials_file, gene_names_file):
""" This function reads the useful information inside the gff_file, essentials_file and
gene_names_file.
For the gff_file and essentials_file extracts the gene coordinates , specifying the chromosome, start ,end
and direction.
For the gene_names_files it translates the systematic name into the standard name.
Parameters
----------
gff_file : .gff3
Annotated genome from Saccharomyces cerevisiae (baker's yeast) (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF_000146045.2_R64/GCF_000146045.2_R64_genomic.gff.gz)
essentials_file : .txt
Essentials genes annotated from yeast , written using the systematic name standard , all in one column
gene_names_file : .txt
This documents lists all the Saccharomyces cerevisiae S288c entries present in
this release of UniProtKB/Swiss-Prot. Yeast (Saccharomyces cerevisiae): entries,
gene names and cross-references to SGD.
Release: 2021_01 of 10-Feb-2021
Returns
-------
dict:
gene_coordinates : a dict specifying for each gene the chromosome number the gene
belongs to, the start gene coordinate, the end gene coordinate and the strand direction ('+' or '-').
dict:
essential_coordinates: a dict specifying for each annotated essential gene the chromosome number the gene
belongs to, the start gene coordinate, the end gene coordinate and the strand direction ('+' or '-').
dict:
aliases_designation: a dict that for each systematic gene name specify the standard gene name.
"""
# Get gene position
gene_coordinates = gene_position(gff_file) #'YAL069W' | ['I', 335, 649], ...
# Get all annotated essential genes
essential_coordinates = {}
with open(essentials_file, "r") as f:
genes = f.readlines()[1:]
for gene in genes:
name = gene.strip("\n")
essential_coordinates[name] = gene_coordinates.get(name).copy()
# Get aliases of all genes
aliases_designation = gene_aliases(gene_names_file)[0] #'YMR056C' \ ['AAC1'], ...
return gene_coordinates, essential_coordinates, aliases_designation
