def open_files(): global annotated_seqs_file, seqs_filtration_file, csv_output_file, extra_tracks_files annotated_seqs_file = open(project_paths.get_annotated_seqs_file_path(), 'rb') seqs_filtration_file = open(project_paths.get_filtered_seqs_file_path(), 'rb') csv_output_file = open(output_file_path, 'wb') if advanced: for track_name, track_file_path in project_paths.get_track_file_paths().items(): extra_tracks_files[track_name] = open(track_file_path, 'rb')
def open_files(): global annotated_seqs_file, seqs_filtration_file, csv_output_file, extra_tracks_files annotated_seqs_file = open(project_paths.get_annotated_seqs_file_path(), 'rb') seqs_filtration_file = open(project_paths.get_filtered_seqs_file_path(), 'rb') csv_output_file = open(output_file_path, 'wb') if advanced: for track_name, track_file_path in project_paths.get_track_file_paths( ).items(): extra_tracks_files[track_name] = open(track_file_path, 'rb')
''' import sys import re import xml.etree.ElementTree as et from StringIO import StringIO from cleavepred import util from cleavepred import project_paths project_paths.dataset_name = 'uniprot' if len(sys.argv) > 1: output_file_path = sys.argv[1] else: output_file_path = project_paths.get_annotated_seqs_file_path() def get_unique(element, xpath): subelements = element.findall(xpath) if len(subelements) == 0: return None if len(subelements) == 1: return subelements[0] else: raise Exception('%d subelements: %s' % (len(subelements), xpath)) def parse_uniprot_xml(raw_xml_path):
''' import sys import re import xml.etree.ElementTree as et from StringIO import StringIO from cleavepred import util from cleavepred import project_paths project_paths.dataset_name = 'uniprot' if len(sys.argv) > 1: output_file_path = sys.argv[1] else: output_file_path = project_paths.get_annotated_seqs_file_path() def get_unique(element, xpath): subelements = element.findall(xpath) if len(subelements) == 0: return None if len(subelements) == 1: return subelements[0] else: raise Exception('%d subelements: %s' % (len(subelements), xpath)) def parse_uniprot_xml(raw_xml_path): raw = util.read_file(raw_xml_path) fixed_raw = re.sub(r'xmlns="[^"]*"', '', raw)