pbs scripts
Simon Brunning
simon at brunningonline.net
Wed Dec 2 09:59:05 EST 2009
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.
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