# -*- coding: utf-8 -*-
from transposonmapper.importing import load_sgd_tab
from transposonmapper.utils import chromosomename_roman_to_arabic
[docs]def sgd_features(filepath=None):
"""This function read the file SGD_features.tab and create a dictionary with useful info for processing
Parameters
----------
filepath : str, optional
filepath of the sgd.tab file , by default None
Returns
-------
dict
A dictionary with the following info:
key:
0. Feature name
value:
0. feature type (l[1])
1. feature qualifier (Verified or Dubious) (l[2])
2. Standard name (l[4])
3. Aliases (separated by '|') (l[5])
4. Parent feature name (typically 'chromosome ...') (l[6])
5. Chromosome (l[8])
6. start coordinate (starting at 0 for each chromosome) (l[9])
7. end coordinate (starting at 0 for each chromosome) (l[10])
This file reads the SGD_features.txt file found at http://sgd-archive.yeastgenome.org/curation/chromosomal_feature/
"""
if filepath == None:
filepath=load_sgd_tab()
arabic_to_roman_dict=chromosomename_roman_to_arabic()[0]
with open(filepath) as f:
lines = f.readlines()
feature_list = []
feature_orf_dict = {}
feature_ars_dict = {}
feature_telomere_dict = {}
feature_ltr_dict = {}
feature_centromere_dict = {}
feature_Xelement_dict = {}
feature_intron_dict = {}
feature_ncrna_dict = {}
feature_ncexon_dict = {}
feature_trna_dict = {}
feature_snorna_dict = {}
feature_teg_dict = {}
feature_5p_utrintron_dict = {}
feature_mas_dict = {}
feature_snrna_dict = {}
feature_rrna_dict = {}
feature_ets_dict = {}
feature_its_dict = {}
feature_oor_dict = {}
feature_telrna_dict = {}
for line in lines:
l = line.strip('\n').split('\t')
if not l[1] in feature_list:
feature_list.append(l[1])
if not l[8].endswith('micron') and not l[8] == '':
chromosome = arabic_to_roman_dict.get(int(l[8]))
if l[1] == 'ORF':
feature_orf_dict[l[3]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'ARS':
feature_ars_dict[l[3]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'telomere':
feature_telomere_dict[l[3]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'long_terminal_repeat':
feature_ltr_dict[l[3]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'centromere':
feature_centromere_dict[l[3]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'X_element':
feature_Xelement_dict[l[3]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'intron':
feature_intron_dict[l[6]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'ncRNA_gene':
feature_ncrna_dict[l[3]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'noncoding_exon':
feature_ncexon_dict[l[6]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'tRNA_gene':
feature_trna_dict[l[3]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'snoRNA_gene':
feature_snorna_dict[l[3]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'transposable_element_gene':
feature_teg_dict[l[3]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'five_prime_UTR_intron':
feature_5p_utrintron_dict[l[6]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'matrix_attachment_site':
feature_mas_dict[l[3]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'snRNA_gene':
feature_snrna_dict[l[3]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'rRNA_gene':
feature_rrna_dict[l[3]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'external_transcribed_spacer_region':
feature_ets_dict[l[6]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'internal_transcribed_spacer_region':
feature_its_dict[l[6]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'origin_of_replication':
feature_oor_dict[l[3]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
elif l[1] == 'telomerase_RNA_gene':
feature_telrna_dict[l[3]] = [l[1], l[2], l[4], l[5], l[6], chromosome, l[9],l[10]]
genomicregions_list = ['ORF', 'ARS', 'Telomere', 'long_terminal_repeat',
'Centromere', 'X_element', 'Intron', 'ncRNA_gene',
'Noncoding_exon', 'tRNA_gene', 'snoRNA_gene',
'transposable_element_gene', 'five_prime_UTR_intron',
'matrix_attachment_site', 'snRNA_gene', 'rRNA_gene',
'external_transcribed_spacer_region',
'internal_transcribed_spacer_region',
'origin_of_replication', 'telomerase_RNA_gene']
return(genomicregions_list, feature_orf_dict, feature_ars_dict, feature_telomere_dict,
feature_ltr_dict, feature_centromere_dict, feature_Xelement_dict, feature_intron_dict,
feature_ncrna_dict, feature_ncexon_dict, feature_trna_dict,
feature_snorna_dict, feature_teg_dict, feature_5p_utrintron_dict,
feature_mas_dict, feature_snrna_dict, feature_rrna_dict,
feature_ets_dict, feature_its_dict, feature_oor_dict,
feature_telrna_dict)
