root/trunk/cartwheel-clients/canal/examples/create-pairwise-analysis.py

#! /usr/bin/env python
"""
A simple example script that shows how to add a pairwise analysis.
"""

# first, add the directory containing 'canalAPI' into sys.path:
import os.path
thisdir = os.path.dirname(__file__)
libdir = os.path.join(thisdir, '../')
libdir = os.path.normpath(libdir)

import sys
if libdir not in sys.path:
    sys.path.insert(0, libdir)

# now, get a connection:
if len(sys.argv) != 4:
    sys.stderr.write('''\

You need to specify a server, a username, and a password
e.g.

    %s http://woodward.caltech.edu/canal/ <user> <pass>

''' % (sys.argv[0],))
    sys.exit(-1)

from canalAPI.xmlrpc import get_xmlrpc_instance

# connect:
conn = get_xmlrpc_instance(sys.argv[1])

# authenticate:
conn.authenticate(sys.argv[2], sys.argv[3])

# finally, create an analysis folder, add sequences, create pairwise
# analysis...

lab = conn.get_current_lab()
folder = lab.create_leaf_folder('my new folder')

seq1 = folder.add_sequence("seq1", "ATGCCGGGNAGGAGATGGT", "DNA")
seq2 = folder.add_sequence("seq2", "GAGAGNAGAGAGAGATATATAGC", "DNA")

pair = folder.add_pair_analysis_group("pairwise group", seq1, seq2)

pair.add_seqcomp_analysis('test seqcomp', 20, 0.7)
pair.add_blastz_analysis('test blastz')
pair.add_lagan_vista_analysis('lagan/vista', 100, 0.7)