import numpy as np
[docs]def add_chromosome_length_inserts(coordinates, ref_names, chr_lengths):
""" For each insertion location, add the length of all previous chromosomes
Parameters
----------
numpy.array
Third output from get_reads(bam)
list
Output from the following :
ref_tid = get_chromosome_names(bam)
ref_names = list(ref_tid.keys())
dict
First output from get_sequence_length(bam)
Returns
-------
numpy.array
For each insertion location, add the length of all previous chromosomes
"""
ll = 0
for ii in range(1,len(ref_names)):
ll += chr_lengths[ref_names[ii-1]]
aa = np.where(coordinates[:,0] == ii + 1)
coordinates[aa,1] = coordinates[aa,1] + ll
return coordinates
[docs]def add_chromosome_length(coordinates, chr_lengths_cumsum, ref_tid_roman):
"""This function returns a dictionary that for every gene , there is the chromosome number
information of where the gene belongs to , the coordinates for the start position, the end position
and the direction of the gene.
Parameters
----------
coordinates : dict
This dictionary is the 1st output from the function read_genes(gff_file, essentials_file, gene_names_file)
chr_lengths_cumsum : dict
This dictionary is the 2nd output from the function get_sequence_length(bam)
ref_tid_roman : dict
This dictionary is the output from
ref_tid_roman = {key: value for key, value in zip(ref_romannums, ref_tid)}, where
ref_romannums = chromosomename_roman_to_arabic()[1] and
ref_tid = get_chromosome_names(bam)
Returns
-------
dict
A dictionary that for every gene , there is the chromosome number information of where the gene belongs to , the coordinates for the start position, the end position
and the direction of the gene.
"""
for key in coordinates:
gene_chrom = ref_tid_roman.get(coordinates.get(key)[0])
coordinates[key][1] = coordinates.get(key)[1] + chr_lengths_cumsum.get(gene_chrom)
coordinates[key][2] = coordinates.get(key)[2] + chr_lengths_cumsum.get(gene_chrom)
return coordinates
