import os
import pkg_resources
[docs]def load_default_files(gff_file=None, essentials_file=None, gene_names_file=None):
"""This function loads some files that have a recurrent use throughout the pipeline.
It will look inside the satay/data_files folder for the files if the input is None.
Otherwise it will return the same input file.
Parameters
----------
gff_file : .gff3, optional
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), by default None
essentials_file : .txt, optional
Essentials genes annotated from yeast , written using the systematic name standard ,
all in one column, by default None
gene_names_file : .txt, optional
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, by default None
Returns
-------
str:
The correct path of the .gff3 input required file for the further analysis.
str:
The correct path of the essential file input required file for the further analysis.
str:
The correct path of the gene_name_file required file for the further analysis.
"""
default_path = pkg_resources.resource_filename("transposonmapper", "data_files/")
if gff_file is None:
gff_file = os.path.join(
default_path, "Saccharomyces_cerevisiae.R64-1-1.99.gff3"
)
if essentials_file is None:
essentials_file = os.path.join(
default_path, "Cerevisiae_AllEssentialGenes_List.txt"
)
if gene_names_file is None:
gene_names_file = os.path.join(default_path, "Yeast_Protein_Names.txt")
return gff_file, essentials_file, gene_names_file
[docs]def load_sgd_tab(sgd_features_file=None):
"""This function loads the file SGD_features.tab
The latest version of the SGD_features.tab file is based on Genome Version R64-2-1.
If a specific file is provided it will output that file , otherwise , if it is set to None then
it will give the standard file provided in the package.
Parameters
----------
sgd_features_file : str, optional
The latest version of the SGD_features.tab file is based on Genome Version R64-2-1., by default None
Returns
-------
str:
The path corresponding to this file in the package
"""
default_path = pkg_resources.resource_filename("transposonmapper", "data_files/")
if sgd_features_file is None:
sgd_features_file = os.path.join(default_path,'SGD_features.tab')
return sgd_features_file
