# =============================================================================
# To import the functions, type:
# import sys
# sys.path.insert(1,r'full\path\to\this\file')
# from essential_genes import list_known_essentials
# =============================================================================
import os
from transposonmapper.importing import load_default_files
[docs]def list_known_essentials(input_files = None, headerlines=3, verbose=True):
"""Get all known essential genes from two different files and combine them in one list.
Input is a list of of paths where files can be found with the known essential genes.
A default list is implemented using two files present in the same folder as this file.
It is expected that the files contain genes in a single column and nothing else.
An option can be set for the number of headerlines, which by default is set to 3.
The output is a list containing all the genes present in all files given in the input.
Note when using the default files: The length of the output list exceed the number of known essential genes as the list sometimes contains both the standard name and the systematic name of a gene.
Parameters
----------
input_files : str, optional
File path for the essential file in your file system, by default None
headerlines : int, optional
by default 3
verbose : bool, optional
To show explanations if True, by default True
"""
if input_files == None:
# If necessary, load default files
gff_file, essential_genes_files, gene_name_file = load_default_files(
gff_file=None, essentials_file=None, gene_names_file=None
)
# Verify presence of files
data_files = {
"gff3": gff_file,
"essentials": essential_genes_files,
"gene_names": gene_name_file,
}
for filetype, file_path in data_files.items():
assert file_path, f"{filetype} not found at {file_path}"
input_files=essential_genes_files
else:
essential_genes_files = input_files
known_essential_gene_list = []
#making sure essential_genes_files is a list
if type(essential_genes_files)!=list:
essential_genes_files=[input_files]
for files in essential_genes_files:
if verbose == True:
print('Reading file :',files)
with open(files) as f:
for header_lines in range(headerlines):
next(f)
for lines in f:
known_essential_gene_list.append(lines.rstrip('\n'))
return(known_essential_gene_list)
# #%%
# if __name__ == '__main__':
# known_essential_gene_list = list_known_essentials()
