import json from pprint import pp from pathlib import Path from Bio import Entrez from typing import Union import re import os import glob import utils from Bio.Entrez.Parser import DictionaryElement, ListElement import utils from Bio import SeqIO from Bio.SeqRecord import SeqRecord from Bio.Entrez.Parser import DictionaryElement, ListElement from Bio.SeqIO.InsdcIO import GenBankIterator Entrez.email = 'carde602@gmail.com' CACHE_DIR = Path('/bio/practica_2/data') from pathlib import Path def count_files(path): file_list = glob.glob(path) num_of_files = len(file_list) return num_of_files def get_xml_from_ncbi(terms): for i in terms: utils.request_search(db='nucleotide',term=i,retmax=1,xml_filename=f'/bio/practica_2/data/{i}.xml') def get_files_in_dir(directory_path): directory_path = Path(directory_path) files = [] for file in directory_path.glob('*'): if file.is_file(): files.append(str(file)) return files def get_id_list(list_of_files): id_list = [] for file in list_of_files: dict = utils.read_xml(file) id_for_list = dict['IdList'][0] id_list.append(id_for_list) return id_list def get_gb_files(list_of_id): for id in list_of_id: utils.request_fetch('nucleotide',id,'gb',f'/bio/practica_2/gb_files/{id}.gb') def rename_files_gb(list_of_gb): for file in list_of_gb: record_iter: GenBankIterator = SeqIO.parse(file, 'gb') for record in record_iter: if record.features: for feature in record.features: if feature.type == "source": name_list = feature.qualifiers["organism"] name = name_list[0] reg_white_space = r'\s' pat_white_space = re.compile(reg_white_space) name = pat_white_space.sub('_', name) reg_name = r'\/([^\/]+)$' pat_name = re.compile(reg_name) file_name = pat_name.search(file).group(1) new_file_name = os.path.dirname(file) + '/' + name + os.path.splitext(file_name)[1] os.rename(file, new_file_name) # def rename_files(directory_path): # list_of_files = get_files_in_dir(directory_path) # list_of_parser_files = [] # for file in list_of_files: # file_parsed:GenBankIterator = SeqIO.parse(file,'gb') # list_of_parser_files.append(file_parsed) # return list_of_parser_files # Main # --------------------------------------------------------------------- this_module: str = __name__ main_module: str = "__main__" if this_module == main_module: # List of term to search for the id list_of_terms = ['Rabies lyssavirus isolate 18018LIB, complete genome','ebolavirus, complete genome','Marburg marburgvirus isolate MARV001, complete genome','Nipah virus, complete genome','Variola virus[ORGN]', 'TREPONEMA PALLIDUM TRIPLET ','Method of Immunization against the 4 serotypes of Dengue fever','Kyasanur forest disease virus isolate W6204 NS5 gene, partial cds'] data_to_count = '/bio/practica_2/data/*' gb_files_to_count = 'practica_2/gb_files/*' data = '/bio/practica_2/data' gb_files = 'practica_2/gb_files' num_of_xml_files_before_search_in_ncbi = count_files(data_to_count) num_of_gb_files_before_search_in_ncbi = count_files(gb_files_to_count) # Get the xml from ncbi print(num_of_xml_files_before_search_in_ncbi) print(num_of_gb_files_before_search_in_ncbi) if num_of_xml_files_before_search_in_ncbi == 0: get_xml_from_ncbi(list_of_terms) print('excecuted: get_xml_from_ncbi') if num_of_xml_files_before_search_in_ncbi > 0: list_of_xml = get_files_in_dir(data) id_list = get_id_list(list_of_xml) print(id_list) get_gb_files(id_list) print('excecuted: get_gb_files') if num_of_gb_files_before_search_in_ncbi > 0: list_of_gb = get_files_in_dir(gb_files) rename_files_gb(list_of_gb) print('excecuted: rename_files_gb')
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