pbs scripts

[Simon Brunning]

2009/12/2 aoife <aoifed88 at hotmail.com>:
> Hi,very new.hoping to incorporate python into my postgrad.
>
> Basically I have 2,000 files.I want to write a script that says:
>
> open each file in turn

If they are in one directory, look at the glob module. If they are in
a bunch of sub-directories, see os.walk(), or <http://bit.ly/5Q5Qiv>.

For looping through the files, see <http://bit.ly/4zvi9P>.

> for each file:
>       open this pbs script and run MUSCLE (a sequence alignment tool)
> on each file

Is MUSCLE a command-line tool? If so, see the subprocess module.

>       close this file

Do you actually need to open the file, or just run a command on it?
Sounds like the latter to me.

>       move on to next file.

Give it a go. Any problems, I'm sure we'd be happy to help.

-- 
Cheers,
Simon B.