Mercurial > repos > bebatut > convert_extract_sequence_file

comparison convert_extract_sequence_file.py @ 1:158642ce204f draft default tip

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planemo upload commit 0a1bbb0870f6b776175151d4bc818c5546731ca8-dirty
author bebatut
date Thu, 28 Apr 2016 08:36:12 -0400
parents 01c2b74b3a21
children
comparison
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0:01c2b74b3a21 1:158642ce204f
40 id_line = get_new_line(input_file, generate_error = False) 40 id_line = get_new_line(input_file, generate_error = False)
41 if id_line == None: 41 if id_line == None:
42 return None 42 return None
43 split_line = id_line[1:].split(' ') 43 split_line = id_line[1:].split(' ')
44 seq_id = split_line[0] 44 seq_id = split_line[0]
45 description = ' '.join(split_line[1:]) 45 description = id_line[1:]
46 new_line = get_new_line(input_file, generate_error = False) 46 new_line = get_new_line(input_file, generate_error = False)
47 seq = '' 47 seq = ''
48 while new_line != None: 48 while new_line != None:
49 if new_line[0] != '>': 49 if new_line[0] != '>':
50 seq += new_line 50 seq += new_line
263 # Other functions 263 # Other functions
264 def save_conserved_records(self,args): 264 def save_conserved_records(self,args):
265 if args.custom_extraction_type == 'True': 265 if args.custom_extraction_type == 'True':
266 to_extract = args.to_extract[1:-1].split(',') 266 to_extract = args.to_extract[1:-1].split(',')
267 with open(args.output_information, 'w') as output_information_file: 267 with open(args.output_information, 'w') as output_information_file:
268 output_information_file.write('\t'.join(to_extract) + '\n') 268 #output_information_file.write('\t'.join(to_extract) + '\n')
269 for record in self.conserved_records: 269 for record in self.conserved_records:
270 extracted_info = record.extract_information(to_extract) 270 extracted_info = record.extract_information(to_extract)
271 string_info = [str(info) for info in extracted_info] 271 string_info = [str(info) for info in extracted_info]
272 string = '\t'.join(string_info) 272 string = '\t'.join(string_info)
273 output_information_file.write(string + '\n') 273 output_information_file.write(string + '\n')