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Expand Toolbox with SBML scrapping app

Merged Clement Frainay requested to merge feature/SBML_scraping into develop
1 unresolved thread

Allows user to extract and format data encapsulated in SBML files

Edited by Clement Frainay

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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)
  • Ca peut être compliqué si on a 50 pathways non ? Est ce que ça serait compliqué d'avoir le parametre "inline" et la lecture d'un fichier avec 1 voie par ligne ?

  • C'est vrai que les cas que j'ai eu c'etait plutot 1 ou 2 pathways, mais effectivement, bcp plus ça deviendrait compliqué, je vais voir pour ajouter l'option fichier

  • 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.

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  • Ludovic Cottret
  • added 1 commit

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  • Clement Frainay added 16 commits

    added 16 commits

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  • Clement Frainay added 3 commits

    added 3 commits

    • 0f3dae33 - handle pathway not found case in extractpathway
    • ab85151a - remove debug print
    • c36a29f3 - fix duplicated refs

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  • Clement Frainay marked this merge request as ready

    marked this merge request as ready

  • Clement Frainay approved this merge request

    approved this merge request

  • Clement Frainay mentioned in commit 3f6a5f4e

    mentioned in commit 3f6a5f4e

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