ask for more information for TPP without GUI

[tiannan]

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!

[Melody Lam]

Tian Nan Ni Hao!

Actually the commands are shown on the GUI result page.
Here are some commonly used commands:

For PeptideProphet

xinteract -Ninteract.pep.xml -p0.05 -l7 -OdAmp -I2 -I3 -I4 -I5 -I6 -
I7 -dDECOY_ abc.pep.xml efg.pep.xml ...
type xinteract only for help and note on the parameters

For ProteinProphet

ProteinProphet interact.pep.xml interact.prot.xml EXCLUDE_ZEROS
protxml2html.pl -file <location of xml interact.prot.xml >

Melody

[Greg Bowersock]

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

[tiannan]

hi Melody, Ni Hao! :>

Thanks for answering the "stupid" question! I should have
noticed the commands!

cheers,
Tiannan

[Matthew Chambers]

Somewhat off-topic, I learned yesterday that NTFS supports symbolic
links starting with Vista:
http://en.wikipedia.org/wiki/NTFS_symbolic_link

-Matt

[Greg Bowersock]

I've played around with those a little, and they are closer to hard-links, and don't work very well. The support is also in Windows 2003 Server, which is where I tried it. Windows calls them Junctions, and there are some free tools out there that will create them for you. Granted I was trying to map a network drive (from an NTFS share) and create a junction to that drive, and that doesn't work at all. It is supposed to work with local disks though, so if you are doing things that way you will be fine. As you know the nice thing about Linux is that you can create a soft-link to a samba/cifs/nfs mounted directory with no problems at all. If Windows would figure out how to do that it would be nice.

 

Greg

[Matthew Chambers]

I knew about junctions, and indeed they are lame. The new tool is
'mklink' and its links are different:
"Unlike a NTFS junction point
<http://en.wikipedia.org/wiki/NTFS_junction_point> (available since
Windows 2000), a symbolic link can also point to a file or remote SMB
<http://en.wikipedia.org/wiki/Server_Message_Block> network path."

So give it another look if you want that functionality. I know I'll use
it sooner rather than later.

-Matt

Greg Bowersock wrote:
> I've played around with those a little, and they are closer to
> hard-links, and don't work very well. The support is also in Windows
> 2003 Server, which is where I tried it. Windows calls them Junctions,
> and there are some free tools out there that will create them for you.
> Granted I was trying to map a network drive (from an NTFS share) and
> create a junction to that drive, and that doesn't work at all. It is
> supposed to work with local disks though, so if you are doing things
> that way you will be fine. As you know the nice thing about Linux is
> that you can create a soft-link to a samba/cifs/nfs mounted directory
> with no problems at all. If Windows would figure out how to do that it
> would be nice.
>
> Greg
>
> On Thu, Oct 22, 2009 at 11:36 AM, Matthew Chambers
> <matthew....@vanderbilt.edu