Mercurial > repos > abims-sbr > blastalign
comparison scripts/S01_phylip2fasta.py @ 5:0d2da4c020dc draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit df6ba874c5e5f0cde12c9253b5c192e4a35f2280
| author | abims-sbr |
|---|---|
| date | Thu, 18 Jan 2018 08:13:26 -0500 |
| parents | 49017ea906b5 |
| children | e0bea88bb09f |
comparison
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| 4:9eb5bb56bf41 | 5:0d2da4c020dc |
|---|---|
| 11 print "put arguments!!" | 11 print "put arguments!!" |
| 12 print "USAGE: S01_phylip2fasta.py INPUT OUTPUT" | 12 print "USAGE: S01_phylip2fasta.py INPUT OUTPUT" |
| 13 """ | 13 """ |
| 14 | 14 |
| 15 ## INPUT | 15 ## INPUT |
| 16 """ | |
| 16 if os.path.isfile(sys.argv[1]) : | 17 if os.path.isfile(sys.argv[1]) : |
| 17 f1 = sys.argv[1] | 18 f1 = sys.argv[1] |
| 18 else: | 19 else: |
| 19 print "No existing phylip file ; exiting ..." | 20 print "No existing phylip file ; exiting ..." |
| 20 exit() | 21 exit() |
| 21 | 22 """ |
| 23 f1 = sys.argv[1] | |
| 22 F1 = open("%s" %f1, 'r') | 24 F1 = open("%s" %f1, 'r') |
| 23 | 25 |
| 24 ## OUTPUT | 26 ## OUTPUT |
| 25 f2 = sys.argv[2] | 27 f2 = sys.argv[2] |
| 26 F2 = open("%s" %f2, 'w') | 28 F2 = open("%s" %f2, 'w') |
| 48 ################### | 50 ################### |
| 49 ### RUN RUN RUN ### | 51 ### RUN RUN RUN ### |
| 50 ################### | 52 ################### |
| 51 | 53 |
| 52 F1.readline() ## jump the first line | 54 F1.readline() ## jump the first line |
| 53 | |
| 54 fichier_txt, c = format(F1) ### DEF1 ### | 55 fichier_txt, c = format(F1) ### DEF1 ### |
| 55 | |
| 56 F2.write(fichier_txt) | 56 F2.write(fichier_txt) |
| 57 | |
| 58 F1.close() | 57 F1.close() |
| 59 F2.close() | 58 F2.close() |