view test/usecase1.py @ 735:632a0708ab33
blocks3d/www: allow blocks not to be continuous
Changes:
* javascript
* blocks_to_html method of AlignmentMixin
* test for blocks viewer (add one non-continuous block)
Currently block can have either "start" and "end" or "positions" attribute,
but not both. "start" and "end" attributes are not deprecated and can be
used if blocks are known to be continuous or while writting blocks
javascript by hands.
close #71
| author |
boris <bnagaev@gmail.com> |
| date |
Fri, 08 Jul 2011 20:21:39 +0200 |
| parents |
07b5351b0b56 |
| children |
ddf85d0a8924 |
line source
2 from allpy import protein
3 from allpy import processors
5 # Create sequences from string representation of sequence body
6 sequence_1 = protein.Sequence.from_string("mkstf", name="E2E4")
7 sequence_2 = protein.Sequence.from_string("mstkfff", description="Longer sequence")
9 # Create alignment from sequences
10 alignment = protein.Alignment()
11 alignment.append_sequence(sequence_1)
12 alignment.append_sequence(sequence_2)
13 alignment.realign(processors.Muscle())
15 # For each sequence, print number of gaps and non-gaps in alignment
16 for row in alignment.rows():
19 for column in alignment.columns:
24 print "%s: %s gaps, %s non-gaps" % (row.sequence.name, gaps, monomers)
26 # Print number of gaps in each column
28 for column in alignment.columns:
30 for sequence in alignment.sequences:
31 if sequence not in column:
33 gaps.append(column_gaps)
34 print " ".join(map(str, gaps))
36 # Write alignment to file
37 alignment.to_file(sys.stdout)
