Software:Out2XML

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(In a nutshell)
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At this point you can delete the .dta and .out files (which are now compressed together in the tgz file) to save disk space. At this point you can delete the .dta and .out files (which are now compressed together in the tgz file) to save disk space.
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 +===Working with Bioworks and the out2linux.pl script===
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 +'''out2linux.pl''' was contributed by a TPP user, Alexandre Panchaud. Documentation coming soon!

Revision as of 23:44, 14 June 2007

Contents

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 out2linux.pl script

out2linux.pl was contributed by a TPP user, Alexandre Panchaud. Documentation coming soon!

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