Software:Out2XML
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Revision as of 21:20, 23 May 2007 Jtasman (Talk | contribs) (adding example for running, from David S's post) Next diff → |
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| ==In a nutshell== | ==In a nutshell== | ||
| Out2XML is part of the processing pipeline. This tool converts Sequest result (in .out files) to pepXML files suitable for use in the TPP. | Out2XML is part of the processing pipeline. This tool converts Sequest result (in .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. | ||
Revision as of 21:20, 23 May 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 (in .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.
