import pkg_resources
import os
[docs]def gene_aliases(gene_information_file=None):
"""Create three dictionaries containing aliases for genes
Input is the path to 'Protein_Names.txt' file downloaded from https://www.uniprot.org/docs/yeast.
If no input is given the file is automatically searched for at thisscriptlocation/../Data_Files/Yeast_Protein_Names.txt.
Output is three dictionaries:
aliases_designation_dict = gene aliases for common names (e.g. Bem1 and Sro1)
aliases_sgd_dict = gene aliases for the search names in SGD (e.g. Bem1 and S000000404)
aliases_swissprot_dict = gene aliases for Swiss Prot.
The keys of the dictionaries are the systematic names of the genes (e.g. YBR200W for Bem1)
Search through lists to get corresponding key:
[key for key, val in aliases.items() if 'TFC3' in val]
Parameters
----------
gene_information_file : str, optional
Input is the path to 'Protein_Names.txt' file downloaded from https://www.uniprot.org/docs/yeast.
If no input is given the file is automatically searched for at Yeast_Protein_Names.txt inside the package, by default None
Returns
-------
dict
gene aliases for common names (e.g. Bem1 and Sro1)
dict
gene aliases for the search names in SGD (e.g. Bem1 and S000000404)
dict
gene aliases for Swiss Prot
"""
if gene_information_file == None:
default_path = pkg_resources.resource_filename("transposonmapper", "data_files/")
gene_information_file = os.path.join(default_path, "Yeast_Protein_Names.txt")
aliases_designation_dict = {}
aliases_sgd_dict = {}
aliases_swissprot_dict = {}
with open(gene_information_file) as f:
lines = f.readlines()
for i in range(
58, len(lines) - 6
): # THE GENES START AT LINE 58 AND STOP 6 LINES BEFORE THE END OF THE FILE.
l = lines[i]
l_list = l.split()
alias_counter = 0
gene_designation_list = []
for names in l_list:
if names.endswith(";"):
gene_designation_list.append(names.strip(";"))
alias_counter += 1
gene_designation_list.append(l_list[alias_counter])
oln_name = l_list[alias_counter + 1]
sgd_name = l_list[alias_counter + 4]
swissprot_name = l_list[alias_counter + 2]
if oln_name == "GAG" or oln_name == "POL":
oln_name = l_list[alias_counter + 2]
sgd_name = l_list[alias_counter + 5]
swissprot_name = l_list[alias_counter + 3]
aliases_designation_dict[oln_name] = gene_designation_list
aliases_sgd_dict[oln_name] = sgd_name
aliases_swissprot_dict[oln_name] = swissprot_name
return (aliases_designation_dict, aliases_sgd_dict, aliases_swissprot_dict)
