W2H: How to post-processed the output files

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With a flood of nice viewers, Java applets and specific post-processors, it becomes important to have a possibility to call these applications from within W2H.

This document explains how to integrate new scripts which are called when a user clicks on an output file in the W2H Output manager window. Together with this document there is also a very simple example script (without any useful meaning) in pp-scripts/map-pp-example.

Also there are other post-processing scripts distributed (by courtesy of people from German Cancer Research Center, Heidelberg, who developed them). These scripts are in subdirectory pp-scripts and they manage to bind output of some applications with SRS service. Please read a README file in that subdirectory.

There are two steps for adding your own data post-processor:

1. configure W2H
2. create (or find) a suitable post-processing program

Configuring W2H

The configuration file Cfg.pl has two variables regarding the post-processing:

$POSTPROCESS_WRAPPER

This variable should contain a suffix which is added to an extension of the output file name to create a name of the post-processing script.

An example: An output file from the Map program has an extension map. $POSTPROCESS_WRAPPER contains -pp. You have to write a script named map-pp.

$POSTPROCESS_PATH

This variable contains a full UNIX path to a directory where all your post-processing scripts are stored. This arrangement saves time. A specialized post-processing script for a given file extension is used only if it is found in this directory.

Creating a post-processing program

You can either find a suitable data viewer or even an applet, or write your own script. In all cases the script must obey the following rules:

• The script name is created from a file extension and from $POSTPROCESS_WRAPPER as described above.
• W2h invokes the script with a file name on the command line. The file name points to an output file clicked on by a user.
• The script should print a document on its standard output. The document will be displayed by W2H in a separate Netscape window. The first line of the document should define a proper content type of the document. An example:

  Content-type: text/html
  one blank line here (!)

  W2H checks it and if a Content-type line is missing it uses a text/plain type.
• If the script encounters an error it can write a message on its standard error output and ends with a non-zero exit code.
• Before starting the post-processing script, W2H sets some environment variables which can be used by the post-processor. Each of these variable starts with letters W2H_ followed by a name of a W2H global user preference (in lower cases). The preferences names used can be found in $HOME/.w2h-www/.w2h-history. The most useful environment variables set are probably:
  • W2H_workdir containing a name of the current working directory
  • W2H_worklist with a name of the current working list
  
  In addition, W2H sets the following environment variables:

  	W2H_BIN_ROOT	value of $BIN_ROOT in Cfg.pl
  	W2H_YA_ROOT	value of $YA_ROOT in Cfg.pl
  	W2H_DOC_ROOT	value of $DOC_ROOT in Cfg.pl
  	W2H_POSTPROCESS_PATH	value of $POSTPROCESS_PATH in Cfg.pl
  	W2H_FILE_EXTENSION	file extension, triggering this post-processor

  
  

Examples

W2H is distributed with some post-processing scripts for the output of one of the following programs of W2H:

• Map
• Factor
• ProSite
• BlastP, BlastN, BlastX, BlastP2, BlastN2, TBlastN, TBlastX, BlastX2, TBlastN2, TBlastX2
• FastA, TFastA
• WordSearch, TWordSearch
• BlastAlign
• Blimps
• FrameSearch
• SW
• HMMSW, HMMFS

The post-processing scripts hyperlink database:sequence pairs in the output files to the suitable database using the SRS program and inserts internal links from the sequence listing at the beginning of many outputs to the alignments in the body of the files. Read the README file and the inslink.pl file for more information.

It would be nice to share more scripts for post-processing of output files. If you have some to offer you can either distribute them using the W2H mailing list, or inform us about them and we can mention them on the W2H Homepage - whatever you prefer.

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