Mercurial > repos > abims-sbr > pairwise

comparison scripts/S03_run_second_blast.py @ 10:cb5f2cc3dedc draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 7d45b8e07bf99420df9b195617515b8002b5eaf3
author abims-sbr
date Fri, 06 Jul 2018 02:51:09 -0400
parents 1e0c547d88fe
children
comparison
equal deleted inserted replaced
9:1e0c547d88fe 10:cb5f2cc3dedc
19 # Traduire les best hits 19 # Traduire les best hits
20 f_name = 'translated_{}'.format(args.query_file) 20 f_name = 'translated_{}'.format(args.query_file)
21 translated_file = open(f_name, 'w') 21 translated_file = open(f_name, 'w')
22 with open(args.query_file, 'r') as file: 22 with open(args.query_file, 'r') as file:
23 for name, seq in itertools.izip_longest(*[file]*2): 23 for name, seq in itertools.izip_longest(*[file]*2):
24 s = Seq(seq.strip('\n').upper(), IUPAC.unambiguous_dna) 24 s = Seq(seq.strip('\n').upper(), IUPAC.ambiguous_dna)
25 translated_file.write(name.strip('\n')+'_orf_1\n') 25 translated_file.write(name.strip('\n')+'_orf_1\n')
26 translated_file.write(s.translate()._data+'\n') 26 translated_file.write(s.translate()._data+'\n')
27 translated_file.write(name.strip('\n')+'_orf_2\n') 27 translated_file.write(name.strip('\n')+'_orf_2\n')
28 translated_file.write(s[1:].translate()._data+'\n') 28 translated_file.write(s[1:].translate()._data+'\n')
29 translated_file.write(name.strip('\n')+'_orf_3\n') 29 translated_file.write(name.strip('\n')+'_orf_3\n')