import os
import numpy as np
import re
from transposonmapper.importing import load_default_files
from transposonmapper.processing import list_known_essentials
[docs]def read_pergene_file(pergenefile):
"""It reads the content of the pergene file , one of the outputs of Transposonmapper
Parameters
----------
pergenefile : str
absolute path to the pergene.txt file , one of the outputs of the transposonmapper module
Returns
-------
list
Gene names list
list
Insertion list
list
Reads list
"""
assert os.path.isfile(pergenefile), 'File not found at: %s' % pergenefile
with open(pergenefile) as f:
lines = f.readlines()[1:] #skip header
genenames_list = [np.nan]*len(lines)
tnpergene_list = [np.nan]*len(lines)
readpergene_list = [np.nan]*len(lines)
line_counter = 0
for line in lines:
line_split = re.split(' |\t', line.strip('\n'))
l = [x for x in line_split if x]
genenames_list[line_counter] = l[0]
tnpergene_list[line_counter] = int(l[1])
readpergene_list[line_counter] = int(l[2])
line_counter += 1
return genenames_list,tnpergene_list,readpergene_list,lines
[docs]def reads_per_insertion(tnpergene_list,readpergene_list,lines):
"""It computes the reads per insertion following the formula:
reads/(insertions-1) if the number of insertions is higher than 5,
if not then the reads per insertion will be 0.
Parameters
----------
tnpergene_list : list
A list with all insertions
readpergene_list : list
A list of the reads
lines : int
Number of genes mapped to in the reference genome
Returns
-------
list
A list containing all the reads per insertions per gene.
"""
readperinspergene_list = [np.nan]*len(lines)
for i in range(len(tnpergene_list)):
if not tnpergene_list[i] < 5:
readperinspergene_list[i] = readpergene_list[i] / (tnpergene_list[i] -1)
else:
readperinspergene_list[i] = 0
return readperinspergene_list
[docs]def essential_genes(genenames_list,lines):
"""It provides a list of essential genes
Parameters
----------
genenames_list : list
A list will al genes names that were mapped to the reference genome
lines : int
Number of genes in total
Returns
-------
list
List of essential genes
"""
_,essential_genes_list,_=load_default_files()
known_essential_gene_list = list_known_essentials(essential_genes_list)
geneessentiality_list = [None]*len(lines)
for i in range(len(genenames_list)):
if genenames_list[i] in known_essential_gene_list:
geneessentiality_list[i] = True
else:
geneessentiality_list[i] = False
return geneessentiality_list
