[Tutor] Parsing data from a set of files iteratively

[Spyros Charonis]

FINAL SOLUTION:

### LOOP OVER DIRECTORY
location = '/Users/spyros/Desktop/3NY8MODELSHUMAN/HomologyModels'
zdata = []
for filename in os.listdir(location):
filename = os.path.join(location, filename)
try:
zdata.extend(extract_zcoord(filename))
except NameError:
print "No such file!"
except SyntaxError:
print "Check Your Syntax!"
except IOError:
print "PDB file NOT FOUND!"
else:
continue

print 'Z-VALUES FOR ALL CHARGED RESIDUES'
print zdata #diagnostic

### WRITE Z-COORDINATE LIST TO A BINARY FILE
import pickle

f1 = open("z_coords1.dat", "wb")
pickle.dump(zdata, f1)
f1.close()

f2 = open("z_coords1.dat", "rb")
zdata1 = pickle.load(f2)
f2.close()

assert zdata == zdata1, "error in pickle/unpickle round trip!"

On Wed, May 30, 2012 at 1:09 AM, Steven D'Aprano <steve at pearwood.info>wrote:

> Steven D'Aprano wrote:
>
>  location = '/Users/spyros/Desktop/**3NY8MODELSHUMAN/**HomologyModels/'
>> zdata = []
>> for filename in os.listdir(location):
>>    zdata.extend(get_zcoords(**filename))
>>
>
I only had the filename and not its path, that's why the system was not
able to locate the file, so
filename = os.path.join(location, filename) was used to solve that.

Many thanks to everyone for their time and efforts!

Spyros

>
>
> Hah, that can't work. listdir returns the name of the file, but not the
> file's path, which means that Python will only look in the current
> directory. You need something like this:
>
>
> location = '/Users/spyros/Desktop/**3NY8MODELSHUMAN/**HomologyModels/'
> zdata = []
> for filename in os.listdir(location):
>    zdata.extend(get_zcoords(os.**path.join(location, filename)))
>
>
> Sorry about that.
>
>
>
>
> --
> Steven
> ______________________________**_________________
> Tutor maillist  -  Tutor at python.org
> To unsubscribe or change subscription options:
> http://mail.python.org/**mailman/listinfo/tutor<http://mail.python.org/mailman/listinfo/tutor>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/tutor/attachments/20120530/bcb8639b/attachment.html>