Hi, I was wondering if we can build models in batch if we are using same template, but different alignment, so for each alignment we have new model. And this could be automated.I have to build around 300 models with same template but different alignment for each model i generate. I would really appreciate if anybody could help me on this. Otherwise it takes a long time if I build them using automodel, as each time i have to change the .ali filename and also the sequence name in there. ThanksVagmita
On 05/02/2011 07:16 AM, Vagmita Pabuwal wrote: > I was wondering if we can build models in batch if we are using same > template, but different alignment, so for each alignment we have new > model. And this could be automated.
Of course - Modeller scripts are just Python scripts, so you can write as complicated a pipeline as you like in Python. Here's a really simple example:
from modeller import * from modeller.automodel import *
log.verbose() env = environ()
model_num = 1 for aln, tmpl in [('align1.ali', 'code1'), ('align2.ali', 'code2'), ('align3.ali', 'code3'): a = automodel(env, alnfile=aln, knowns=tmpl, sequence='seq') a.starting_model = a.ending_model = model_num a.make() model_num += 1
Ben Webb, Modeller Caretaker
participants (2)
-
Modeller Caretaker -
Vagmita Pabuwal