from ..utils import chromosomename_roman_to_arabic
import pkg_resources
import os
[docs]def chromosome_position(gff_file):
"""Get the start and end position of each chromosome and determine their respective length.
Input is a .gff file downloaded from https://www.ensembl.org/Saccharomyces_cerevisiae/Info/Index
Output are three dictionaries for length, start and end position. All dictionaries have keys representing the chromosome number in roman numerals.
To get all dictionaries, use: 'a,b,c, chromosome_and_gene_position.chromosome_position()'.
'a' = chromosome length
'b' = chromosome start position
'c' = chromosome end position
Parameters
----------
gff_file : str
The file path of a .gff file downloaded from https://www.ensembl.org/Saccharomyces_cerevisiae/Info/Index
Returns
-------
dict
A dictionary relating each chromosome with its length
dict
A dictionary relating each chromosome with its start position
dict
A dictionary relating each chromosome with its end position
"""
if gff_file==None:
default_path = pkg_resources.resource_filename("transposonmapper", "data_files/")
gff_file = os.path.join(
default_path, "Saccharomyces_cerevisiae.R64-1-1.99.gff3"
)
# Get roman to arabic dictionary
roman_to_arabic = chromosomename_roman_to_arabic()[1]
# GET END POSITIONS OF THE CHROMOSOMES FROM THE GFF FILE AND STORE THEM IN A DICTIONARY
chr_length_dict = {}
chr_length_list = []
with open(gff_file) as f:
line_counter = 0
next(f)
while line_counter < 17:
lines = f.readline()
chr_line_list = lines.strip("\n").replace(" ", "\t").split("\t")
chr_number = chr_line_list[3]
# if chr_number != 'Mito':
chr_length = int(chr_line_list[5])
chr_length_list.append(chr_length)
chr_length_dict[chr_number] = chr_length
line_counter += 1
# DETERMINE START AND END POSITION OF EACH OF THE CHROMOSOMES
chr_start_pos_dict = {}
chr_end_pos_dict = {}
counter = 0
for roman in roman_to_arabic.keys():
chr_start_pos_dict[roman] = sum(chr_length_list[:counter]) + 1
chr_end_pos_dict[roman] = sum(chr_length_list[: counter + 1])
if roman == "I":
chr_start_pos_dict[roman] = 1
counter += 1
return (chr_length_dict, chr_start_pos_dict, chr_end_pos_dict)
