search

jamesscottbrown / sbml-diff

sbml-diff is a tool for visually representing a single SBM model, or for visually comparing 2 or more SBML models.
http://sysos.eng.ox.ac.uk/tebio/sbml-diff
BSD 3-Clause "New" or "Revised" License
2 stars 1 forks source link

broken dot file after performing diff on multiple SBML files with optional arguments #2

Closed tramyn closed 7 years ago

tramyn commented 7 years ago

Running this command WITH optional arguments doesn’t allow me to view the output dot file:
python sbml-diff.py --params --kinetics --outfile result2.dot /Users/tramynguyen/Documents/GSoC_2016/sbml-diff/test/assignmentRuleModel.xml /Users/tramynguyen/Documents/GSoC_2016/sbml-diff/test/modifiedKineticLaw.xml /Users/tramynguyen/Documents/GSoC_2016/sbml-diff/test/modifiedParameter.xml /Users/tramynguyen/Documents/GSoC_2016/sbml-diff/test/modifiedIdModel.xml /Users/tramynguyen/Documents/GSoC_2016/sbml-diff/test/modifiedParameterValue.xml /Users/tramynguyen/Documents/GSoC_2016/sbml-diff/test/modifiedSBOTermModel.xml

However, running this command WITHOUT optional arguments will generate a working dot file to view:
python sbml-diff.py --outfile result2.dot /Users/tramynguyen/Documents/GSoC_2016/sbml-diff/test/assignmentRuleModel.xml /Users/tramynguyen/Documents/GSoC_2016/sbml-diff/test/modifiedKineticLaw.xml /Users/tramynguyen/Documents/GSoC_2016/sbml-diff/test/modifiedParameter.xml /Users/tramynguyen/Documents/GSoC_2016/sbml-diff/test/modifiedIdModel.xml /Users/tramynguyen/Documents/GSoC_2016/sbml-diff/test/modifiedParameterValue.xml /Users/tramynguyen/Documents/GSoC_2016/sbml-diff/test/modifiedSBOTermModel.xml

jamesscottbrown commented 7 years ago

What's going on here is that when --params or --kinetics are specified, sbml-diff assumes you only want the corresponding tables, not the DOT output. The rationale for this is that you probably want to process DOT output and tables separately, so it makes sense to request them with separate invocations of the sbml-diff.

The--outfile option redirects all output to the specified file. So your first command doesn't produce a DOT file at all - it produces a text file containing the two tables [or one table, before issue #1 was resolved].

tramyn commented 7 years ago

@jamesscottbrown perfect! I am getting the two tables just as you described.