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Getting the software

This software is included in the current TPP distribution.

In a nutshell

Out2XML is part of the processing pipeline. This tool converts Sequest result files (.out files) to pepXML files suitable for use in the TPP.

Running Out2XML

Note: in almost all cases this program will be run for you automatically, either throught the TPP GUI or the xinteract command.

Converting Sequest results to TPP input files

The TPP will require a .tgz archive of all .dta (spectra input) and .out (sequest search result) files, as well as a pepXML (.xml) file.

This example is based on Cygwin but behaves exactly the same under linux.

To run Out2XML open and cygwin terminal and run the command:

Out2XML /cygdrive/c/Inetpub/wwwroot/ISB/data/full/path/to/data 1

This will create a pepXML file called: /cygdrive/c/Inetpub/wwwroot/ISB/data/full/path/to/data.xml

To generate the tgz file run the following cygwin commands:

cd /cygdrive/c/Inetpub/wwwroot/ISB/data/full/path/to/data
find . -name "*" -maxdepth 1 -depth | tar czf ../data.tgz --files-from -
cd ..

At this point you can delete the .dta and .out files (which are now compressed together in the tgz file) to save disk space.

Working with Bioworks and the script

Why is a programm intended to help with Sequest search using Bioworks Browser on a Windows computer and TPP on a Linux server. When performing the search with Bioworks browser, the params file as well as the OUT files do not have a compatible database link for the TPP. Basically, DB location is something like D:\path\to\folder\containing\db\mydb.fasta while it should be /link/to/folder/containing/db/mydb.fasta if running TPP on Linux. Thus, viewing of protein sequences in the TPP is impossible.

What is it doing? creates a new params file called sequest.params based on the existing params file and converts the DB link to a linux compatible db link in the newly created params file. As well, it converts this link in all OUT files. Finally,it creates a pepXML file using Out2XML.

How it works:

1. Perform Sequest search using Bioworks browser.

2. Transfer directories containing DTAs, OUTs and the PARAMS file to your linux server.

3. Transfer DB used for the search to your DBs location on the Linux server.

4. Run

Usage: <databasepath> <outdirectory>

Ex: /usr/local/tpp/html/data/databasedirectory/database.fasta outdirectory              --> single directory
   for i in */; do /usr/local/tpp/html/data/databasedirectory/database.fasta $i; done  --> multiple directories

Download at [1]

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