Expand Toolbox with SBML scrapping app
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Allows user to extract and format data encapsulated in SBML files
Edited by Clement Frainay
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added met4j-toolbox label
requested review from @ludovic.cottret
assigned to @clement.frainay
added 1 commit
- a9510ada - [Toolbox] new app for sub-SBML creation from pathway selection
7 import fr.inrae.toulouse.metexplore.met4j_io.jsbml.writer.JsbmlWriter; 8 import fr.inrae.toulouse.metexplore.met4j_io.jsbml.writer.Met4jSbmlWriterException; 9 import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.AbstractMet4jApplication; 10 import org.kohsuke.args4j.Option; 11 12 import java.io.IOException; 13 14 public class ExtractPathways extends AbstractMet4jApplication { 15 16 @Option(name = "-i", usage = "input SBML file", required = true) 17 public String inputPath = null; 18 19 @Option(name = "-o", usage = "output SBML file", required = true) 20 public String outputPath = null; 21 22 @Option(name = "-p", usage = "pathway identifiers, separated by \"+\" sign if more than one", required = true) Après réflexion je me demande si ça pourrait pas rester une app simple "je veux le sbml du pathway X", et pour des selection plus complexe ou plus lourde, faire une autre app plus générique qui prends un fichier avec des listes d'id d'entrées (pathways mais aussi compounds ou reaction) pour filtrer un sbml avec des removeOnCascade.
- Resolved by Clement Frainay
added 16 commits
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9b494617...bf25b558 - 14 commits from branch
develop
- 27dbaa7a - Merge branch 'develop' into feature/SBML_scraping
- 25721e31 - update jsbmlReader call
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9b494617...bf25b558 - 14 commits from branch
mentioned in commit 3f6a5f4e
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