On 19/05/12 12:42, Spyros Charonis wrote:
I have tried the following two snippets which both results in the same
error
import os, glob
os.chdir('users/spyros/desktop/3NY8MODELSHUMAN/')
homology_models = glob.glob('*.pdb')
for i in range(len(homology_models)):
python serialize_PIPELINE_models.py homology_models[i]
OK, now we see the problem.
You are trying to invoke the interpreter from within
the interpreter. You don't do that.
Instead you need to call the functions defined inside
serialize_PIPELINE_models.py from your script. To do that
you will need to import serialize_PIPELINE_models.py using
import serialize_PIPELINE_models
or, since its a long name:
import serialize_PIPELINE_models as spm
Than you can access the code functions inside using
spm.serialise(filename)
Or whatever the functions inside serialize_PIPELINE_models.py are.
Another thing which makes life easier is to use the for loop differently.
Instead of:
> homology_models = glob.glob('*.pdb')
> for i in range(len(homology_models)):
Just use:
for fn in glob.glob('*.pdb'):
spm.serialise(fn)
But you will first need to ensure that the code inside
serialize_PIPELINE_models.py is available to use as functions.
The other option of course is to miss out Python at this level and write
a bash script to call Python. It would look something like:
#!/bin/bash
###########################
cd users/spyros/desktop/3NY8MODELSHUMAN/
for file in *.pdb
do
python serialize_PIPELINE_models.py $file
done
############################
Which might be the simplest thing if the serialize_PIPELINE_models.py
already works as you require.
--
Alan G
Author of the Learn to Program web site
http://www.alan-g.me.uk/
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