[Bio] / RecoElemSBW / fixSbmlForCytoScape Repository:
ViewVC logotype

View of /RecoElemSBW/fixSbmlForCytoScape

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.1 - (download) (annotate)
Tue Sep 23 20:22:29 2003 UTC (16 years, 1 month ago) by efrank
Branch: MAIN
CVS Tags: HEAD
SbwFactory:
	more fixes for writing SBML.

fixSbmlForCytoScape:

#
# libSbml-2.0.1 generates level 2 sbml.  Cytoscape only reads level 1.
# This sed script doesn't really convert 2 to 1.  It does enough hacks
# on the sbml to make it possible for cytoscape to read it.
#
# A better approach all around would be to generate a SIF file.
#

#!/bin/sh
#
# libSbml-2.0.1 generates level 2 sbml.  Cytoscape only reads level 1.
# This sed script doesn't really convert 2 to 1.  It does enough hacks
# on the sbml to make it possible for cytoscape to read it.
#
# A better approach all around would be to generate a SIF file.
#


cat <<END
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level1" version="1" level="1"
xmlns:sbedit="http://www.sbml.org/2002/ns/sbedit"
xmlns:html="http://www.w3.org/1999/xhtml">
END

tail +3 $1 | sed -e 's/species id/specie id/g' -e 's/id=""//g' -e 's/speciesRef/specieRef/g' -e 's/species=/specie=/g' -e 's#\(<reaction id=.*[0-9]\"\)>#\1 reversible=\"true\">#g' 

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3