Mercurial > repos > abims-sbr > pairwise
changeset 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 | ae65822c1fb7 |
| files | scripts/S01_run_first_blast.py scripts/S03_run_second_blast.py |
| diffstat | 2 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/scripts/S01_run_first_blast.py Tue Jul 03 10:52:31 2018 -0400 +++ b/scripts/S01_run_first_blast.py Fri Jul 06 02:51:09 2018 -0400 @@ -34,7 +34,7 @@ translated_file = open(name, 'w') with open(file, 'r') as file: for name, seq in itertools.izip_longest(*[file]*2): - s = Seq(seq.strip('\n').upper(), IUPAC.unambiguous_dna) + s = Seq(seq.strip('\n').upper(), IUPAC.ambiguous_dna) translated_file.write(name.strip('\n')+'_orf_1\n') translated_file.write(s.translate()._data+'\n') translated_file.write(name.strip('\n')+'_orf_2\n') @@ -62,7 +62,7 @@ print "Pair of species:" print pairwise - sp1, sp2 = pairwise[0].split('_')[1], pairwise[1].split('_')[1] + sp1, sp2 = pairwise[0].split('_')[1], pairwise[1].split('_')[1] #rename 'translated_Xx_transcriptom.fasta' sub_directory_name = sp1 + '_' + sp2 os.mkdir('./blast_%s' %sub_directory_name) @@ -167,4 +167,4 @@ #os.system('mv matches_blast2_%s ./blast_%s' %(sub_directory_name, sub_directory_name)) if __name__ == "__main__": - main() \ No newline at end of file + main()
--- a/scripts/S03_run_second_blast.py Tue Jul 03 10:52:31 2018 -0400 +++ b/scripts/S03_run_second_blast.py Fri Jul 06 02:51:09 2018 -0400 @@ -21,7 +21,7 @@ translated_file = open(f_name, 'w') with open(args.query_file, 'r') as file: for name, seq in itertools.izip_longest(*[file]*2): - s = Seq(seq.strip('\n').upper(), IUPAC.unambiguous_dna) + s = Seq(seq.strip('\n').upper(), IUPAC.ambiguous_dna) translated_file.write(name.strip('\n')+'_orf_1\n') translated_file.write(s.translate()._data+'\n') translated_file.write(name.strip('\n')+'_orf_2\n') @@ -42,4 +42,4 @@ exit() if __name__ == "__main__": - main() \ No newline at end of file + main()