This is the perl script that I use to process multiple sequest files. I have
a different one that uses iProphet that I am still working out some
parameters, but this one I've been using for years. It takes the following
commandline arguments: a text file with the mzXML files to process (1 per
line), the full path to the database used for the search, and a directory
under the tpp_root to place the processed files. You'll need to change the
directories in the script for where your mzXML and sequest results are
located, and if you are using windows, you won't be able to use the
soft-links, so that will require some changes also.
#!/usr/bin/perl
$xml = $ARGV[0];
$db = $ARGV[1];
$dir = $ARGV[2];
open(XML, "< $xml") or die "Couldn't open file list: $xml\n";
while ($line=<XML>) {
@val = split /\./,$line;
$file = @val[0];
system("rm $dir/$file");
system("rm $dir/$file.mzXML");
system("rm $file.mzXML");
system("rm $dir/$file.pep.xml");
system("ln -s /home/fs2/data/mzXML/$file.mzXML $dir/$file.mzXML");
system("ln -s /home/fs2/sequest/$file $dir/$file");
system("./bin/Out2XML /home/TPP/tpp/$dir/$file 1");
system("./bin/InteractParser $dir/int-$file-sequest.pep.xml
$dir/$file.pep.xml");
system("./bin/PeptideProphetParser $dir/int-$file-sequest.pep.xml");
system("./bin/RefreshParser $dir/int-$file-sequest.pep.xml $db");
system("./bin/ProteinProphet $dir/int-$file-sequest.pep.xml
$dir/int-$file-sequest.shtml XML_INPUT");
system("rm $dir/$file.tgz");
system("mv $dir/$file.mzXML .");
}
exit;
Greg
On Wed, Oct 21, 2009 at 9:17 PM, tiannan <tiannan....@gmail.com> wrote:
>
> hi there,
>
> I began to use TPP with GUI. It was a perfect experience. But
> high throughput data sets requires me to process the data more
> efficiently. I used to avoid mouse clicking using DOS or perl scripts.
>
> Here I'm asking, can anybody provide more DOS commands or perl
> scripts to process data files using TPP, such as the commands for
> convert raw to mzXML, run PeptideProphet, ProteinProphet? (I can only
> find one in the wiki tutorial).
>
> Thanks a lot!
>
> >
>
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