Skip to content
Snippets Groups Projects

Expand Toolbox with SBML scrapping app

Merged Expand Toolbox with SBML scrapping app
feature/SBML_scraping into develop
1 unresolved thread
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

Merge request reports

Loading
Loading

Activity

Filter activity
  • Approvals
  • Assignees & reviewers
  • Comments (from bots)
  • Comments (from users)
  • Commits & branches
  • Edits
  • Labels
  • Lock status
  • Mentions
  • Merge request status
  • Tracking
met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/attributes/ExtractPathways.java 0 → 100644
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)
  • Ludovic Cottret
    Ludovic Cottret @ludovic.cottret ·
    Owner

    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 ?

  • Clement Frainay
    Clement Frainay @clement.frainay ·
    Author Owner

    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

  • Clement Frainay
    Clement Frainay @clement.frainay ·
    Author Owner

    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.

  • Please register or sign in to reply
  • Ludovic Cottret
  • Clement Frainay added 1 commit

    added 1 commit

    Compare with previous version

  • Clement Frainay added 16 commits

    added 16 commits

    Compare with previous version

  • Clement Frainay added 3 commits

    added 3 commits

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

    Compare with previous version

  • 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

  • Clement Frainay merged

    merged

    • Please register or sign in to reply