Mercurial > repos > abims-sbr > blastalign
comparison scripts/S01_phylip2fasta.py @ 6:e0bea88bb09f draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 76e603ecd0118c8060d972b675a13db858956eb6
| author | abims-sbr |
|---|---|
| date | Thu, 18 Jan 2018 09:02:24 -0500 |
| parents | 0d2da4c020dc |
| children |
comparison
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| 5:0d2da4c020dc | 6:e0bea88bb09f |
|---|---|
| 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 """ | |
| 17 if os.path.isfile(sys.argv[1]) : | 16 if os.path.isfile(sys.argv[1]) : |
| 18 f1 = sys.argv[1] | 17 f1 = sys.argv[1] |
| 19 else: | 18 else: |
| 20 print "No existing phylip file ; exiting ..." | 19 print "No existing phylip file ; exiting ..." |
| 21 exit() | 20 exit() |
| 22 """ | 21 |
| 23 f1 = sys.argv[1] | |
| 24 F1 = open("%s" %f1, 'r') | 22 F1 = open("%s" %f1, 'r') |
| 25 | 23 |
| 26 ## OUTPUT | 24 ## OUTPUT |
| 27 f2 = sys.argv[2] | 25 f2 = sys.argv[2] |
| 28 F2 = open("%s" %f2, 'w') | 26 F2 = open("%s" %f2, 'w') |
| 50 ################### | 48 ################### |
| 51 ### RUN RUN RUN ### | 49 ### RUN RUN RUN ### |
| 52 ################### | 50 ################### |
| 53 | 51 |
| 54 F1.readline() ## jump the first line | 52 F1.readline() ## jump the first line |
| 53 | |
| 55 fichier_txt, c = format(F1) ### DEF1 ### | 54 fichier_txt, c = format(F1) ### DEF1 ### |
| 55 | |
| 56 F2.write(fichier_txt) | 56 F2.write(fichier_txt) |
| 57 | |
| 57 F1.close() | 58 F1.close() |
| 58 F2.close() | 59 F2.close() |