allpy
annotate test/test.py @ 121:0903179f8c34
lib::block fix geometrical_core -- pass test
graph::bron_kerbosh fix bug with timeout
| author | boris <bnagaev@gmail.com> |
|---|---|
| date | Sat, 23 Oct 2010 23:06:48 +0400 |
| parents | 5e7851709c95 |
| children | 48dc5974eead |
| rev | line source |
|---|---|
| bnagaev@98 | 1 import sys |
| bnagaev@83 | 2 |
| bnagaev@83 | 3 from allpy.lib.project import Project |
| bnagaev@121 | 4 from allpy.lib.block import Block |
| bnagaev@83 | 5 |
| bnagaev@120 | 6 p = Project(open('1jcc_in.fasta')) |
| bnagaev@83 | 7 print "alignment length: %i" % len(p) |
| bnagaev@110 | 8 print "sequence: %s" % str(p.sequences[0]) |
| bnagaev@83 | 9 |
| bnagaev@120 | 10 p.sequences[0].pdb_chain_add(open('1jcc.pdb'), '1jcc', 'B') |
| bnagaev@120 | 11 p.sequences[1].pdb_chain_add(open('1kfm.pdb'), '1kfm', 'A') |
| bnagaev@120 | 12 |
| bnagaev@121 | 13 b = Block(p) |
| bnagaev@121 | 14 print b.geometrical_core() |
| bnagaev@121 | 15 |
| bnagaev@110 | 16 #~ p.muscle_align() |
| bnagaev@110 | 17 #~ p.save_fasta(sys.stdout) |