from transposonmapper.processing.chromosome_names_in_files import chromosome_name_bedfile
from transposonmapper.properties.get_chromosome_position import chromosome_position
import numpy as np
[docs]def summed_chr(chr_length_dict):
"""Create a dictionary where each value is the cumulative sum of all bp in each chromosomes
Parameters
----------
chr_length_dict : dict
A dictionary describing the length of each chromosome.
Returns
-------
dict
A dictionary where each value corresponds to the cumulative sum of the previous chromosomes lengths.
"""
chrom_list = ['I', 'II', 'III', 'IV', 'V', 'VI', 'VII', 'VIII', 'IX', 'X', 'XI', 'XII', 'XIII', 'XIV', 'XV', 'XVI']
summed_chr_length_dict = {}
summed_chr_length = 0
for c in chrom_list:
summed_chr_length_dict[c] = summed_chr_length
summed_chr_length += chr_length_dict.get(c)
return summed_chr_length_dict
[docs]def length_genome(chr_length_dict):
"""Output the length of the genome in bp
Parameters
----------
chr_length_dict : dict
A dictionary describing the length of each chromosome.
Returns
-------
int
The length of the genome
"""
chrom_list = ['I', 'II', 'III', 'IV', 'V', 'VI', 'VII', 'VIII', 'IX', 'X', 'XI', 'XII', 'XIII', 'XIV', 'XV', 'XVI']
l_genome = 0
for chrom in chrom_list:
l_genome += int(chr_length_dict.get(chrom))
return l_genome
[docs]def middle_chrom_pos(chr_length_dict):
"""Defines the middle poit of each chromosome
Parameters
----------
chr_length_dict : dict
A dictionary describing the length of each chromosome.
Returns
-------
list
A list describing for each chromosome the middle point.
"""
summed_chr_length_dict=summed_chr(chr_length_dict)
l_genome=length_genome(chr_length_dict)
middle_chr_position = []
c1 = summed_chr_length_dict.get('I')
for c in summed_chr_length_dict:
if not c == 'I':
c2 = summed_chr_length_dict.get(c)
middle_chr_position.append(c1 + (c2 - c1)/2)
c1 = c2
c2 = l_genome
middle_chr_position.append(c1 + (c2 - c1)/2)
return middle_chr_position
[docs]def counts_genome(variable,bed_file,gff_file):
"""Counts of reads or the transposons per chromosomes
Parameters
----------
variable : str
"transposons" or "reads"
bed_file : str
absolute path of the location of the bedfile
gff_file : str
absolute path of the location of the gff file
Returns
-------
numpy.ndarray
An array of the length of the genome with the counts of each variable per location in the genome.
"""
with open(bed_file) as f:
lines = f.readlines()
chrom_names_dict, chrom_start_index_dict, chrom_end_index_dict= chromosome_name_bedfile(bed_file)
chr_length_dict, chr_start_pos_dict, chr_end_pos_dict = chromosome_position(gff_file)
summed_chr_length_dict=summed_chr(chr_length_dict)
l_genome=length_genome(chr_length_dict)
allcounts_list = np.zeros(l_genome)
if variable == "transposons":
for line in lines[chrom_start_index_dict.get("I"):chrom_end_index_dict.get("XVI")+1]:
line = line.strip('\n').split()
chrom_name = [k for k,v in chrom_names_dict.items() if v == line[0].replace("chr",'')][0]
allcounts_list[summed_chr_length_dict.get(chrom_name) + int(line[1])-1] += 1
elif variable == "reads":
for line in lines[chrom_start_index_dict.get("I"):chrom_end_index_dict.get("XVI")+1]:
line = line.strip('\n').split()
chrom_name = [k for k,v in chrom_names_dict.items() if v == line[0].replace("chr",'')][0]
allcounts_list[summed_chr_length_dict.get(chrom_name) + int(line[1])-1] += (int(line[4])-100)/20
return allcounts_list
[docs]def binned_list(allcounts_list,bar_width):
"""A binned list for a histogram of the counts
Parameters
----------
allcounts_list : numpy.ndarray
Output of the counts_genome function
bar_width : float
It could be a function of the length of the genome e.g. bar_width=l_genome/1000
Returns
-------
list
Binned list
"""
allcounts_binnedlist = []
val_counter = 0
sum_values = 0
for n in range(len(allcounts_list)):
if int(val_counter % bar_width) != 0:
sum_values += allcounts_list[n]
elif int(val_counter % bar_width) == 0:
allcounts_binnedlist.append(sum_values)
sum_values = 0
val_counter += 1
allcounts_binnedlist.append(sum_values)
return allcounts_binnedlist
