allpy
annotate test/test.py @ 310:9ad22a1848fc
Added calls to super to all classes in allpy.base
The calls are not exactly correct.
This WILL fail in certain inheritance situations.
There are two bad situations:
* inheritance from object; __init__ of object does not accept any arguments,
so it is not compatible with interface of any of our classes
* inheritance of Block(Alignment). The situation here is relatively easy to
fix: we should force compatibility of function interfaces for Block and
Alignment.
| author | Daniil Alexeyevsky <me.dendik@gmail.com> |
|---|---|
| date | Thu, 16 Dec 2010 21:08:03 +0300 |
| parents | fb3164f03984 |
| children | faa7e19bffd9 |
| rev | line source |
|---|---|
| bnagaev@98 | 1 import sys |
| bnagaev@83 | 2 |
| me@191 | 3 from allpy.alignment import Alignment |
| me@191 | 4 from allpy.block import Block |
| bnagaev@83 | 5 |
| bnagaev@175 | 6 p = Alignment(open('test.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@130 | 14 GCs = b.geometrical_cores(ac_new_atoms=0.00, ac_count=-1) |
| bnagaev@128 | 15 b.save_fasta(sys.stdout) |
| bnagaev@134 | 16 for i, GC in enumerate(GCs): |
| bnagaev@134 | 17 GC.save_xstring(sys.stdout, i) |
| bnagaev@121 | 18 |
| bnagaev@110 | 19 #~ p.muscle_align() |
| bnagaev@110 | 20 #~ p.save_fasta(sys.stdout) |