Re: [modeller_usage] modelling multiple sequences in one go
To:
Subject: Re: [modeller_usage] modelling multiple sequences in one go
From: Modeller Caretaker <>
Date: Tue, 08 Apr 2008 11:51:58 -0700
Cc:
navkaranj wrote:
I want to know that if I have, say about 10 target sequences that I want
to model, each with a corresponding template structure, what is the
sript that I will have to follow in order to model all of them in one
run? Instead of 10 different scripts which make things cumbersome, I
want to combine the result of all in one script in one run.
Sure, you could do something like that very easily in Python. Most
simply, you could just concatenate your scripts:
from modeller import *
from modeller.automodel import *
env = environ()
a = automodel(env, alnfile='align1.ali', knowns='known1',
sequence='seq1)
a.make()
a = automodel(env, alnfile='align2.ali', knowns='known2',
sequence='seq2')
a.make()
Alternatively, you could write a simple Python wrapper function to call
for each model, e.g.
from modeller import *
from modeller.automodel import *
def build_model(env, alnfile, knowns, sequence):
a = automodel(env, alnfile=alnfile, knowns=knows,
sequence=sequence)
a.make()
env = environ()
for (aln, knowns, sequence) in (('align1.ali', 'known1', 'seq1'),
('align2.ali', 'known2', 'seq2')):
build_model(env, aln, knowns, sequence)
Or... you could use sys.argv to populate alnfile, knowns, sequence, and
then use the same Python script to build different models, specifying
the parameters on the command line.
As regards your other question, you can put in an os.chdir call before
each automodel run, to build models in different directories.