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Annotation of /RecoElemSBW/fixSbmlForCytoScape

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Revision 1.1 - (view) (download)

1 : efrank 1.1 #!/bin/sh
2 :     #
3 :     # libSbml-2.0.1 generates level 2 sbml. Cytoscape only reads level 1.
4 :     # This sed script doesn't really convert 2 to 1. It does enough hacks
5 :     # on the sbml to make it possible for cytoscape to read it.
6 :     #
7 :     # A better approach all around would be to generate a SIF file.
8 :     #
9 :    
10 :    
11 :     cat <<END
12 :     <?xml version="1.0" encoding="UTF-8"?>
13 :     <sbml xmlns="http://www.sbml.org/sbml/level1" version="1" level="1"
14 :     xmlns:sbedit="http://www.sbml.org/2002/ns/sbedit"
15 :     xmlns:html="http://www.w3.org/1999/xhtml">
16 :     END
17 :    
18 :     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'

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