Mercurial > repos > abims-sbr > pairwise
comparison scripts/S01_run_first_blast.py @ 10:cb5f2cc3dedc draft
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
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| 9:1e0c547d88fe | 10:cb5f2cc3dedc |
|---|---|
| 32 name = 'translated_%s' %file | 32 name = 'translated_%s' %file |
| 33 in_files_translated.append(name) | 33 in_files_translated.append(name) |
| 34 translated_file = open(name, 'w') | 34 translated_file = open(name, 'w') |
| 35 with open(file, 'r') as file: | 35 with open(file, 'r') as file: |
| 36 for name, seq in itertools.izip_longest(*[file]*2): | 36 for name, seq in itertools.izip_longest(*[file]*2): |
| 37 s = Seq(seq.strip('\n').upper(), IUPAC.unambiguous_dna) | 37 s = Seq(seq.strip('\n').upper(), IUPAC.ambiguous_dna) |
| 38 translated_file.write(name.strip('\n')+'_orf_1\n') | 38 translated_file.write(name.strip('\n')+'_orf_1\n') |
| 39 translated_file.write(s.translate()._data+'\n') | 39 translated_file.write(s.translate()._data+'\n') |
| 40 translated_file.write(name.strip('\n')+'_orf_2\n') | 40 translated_file.write(name.strip('\n')+'_orf_2\n') |
| 41 translated_file.write(s[1:].translate()._data+'\n') | 41 translated_file.write(s[1:].translate()._data+'\n') |
| 42 translated_file.write(name.strip('\n')+'_orf_3\n') | 42 translated_file.write(name.strip('\n')+'_orf_3\n') |
| 60 if args.method == 'diamond': | 60 if args.method == 'diamond': |
| 61 for pairwise in list_pairwise: | 61 for pairwise in list_pairwise: |
| 62 print "Pair of species:" | 62 print "Pair of species:" |
| 63 print pairwise | 63 print pairwise |
| 64 | 64 |
| 65 sp1, sp2 = pairwise[0].split('_')[1], pairwise[1].split('_')[1] | 65 sp1, sp2 = pairwise[0].split('_')[1], pairwise[1].split('_')[1] #rename 'translated_Xx_transcriptom.fasta' |
| 66 sub_directory_name = sp1 + '_' + sp2 | 66 sub_directory_name = sp1 + '_' + sp2 |
| 67 os.mkdir('./blast_%s' %sub_directory_name) | 67 os.mkdir('./blast_%s' %sub_directory_name) |
| 68 | 68 |
| 69 print 'Running first blast with Diamond ...' | 69 print 'Running first blast with Diamond ...' |
| 70 | 70 |