Convert¶

mapFormatConversion(fileNameIn, inputFormat, outputFormat)[source]¶

Convert one metabolic map format into another using external tools

Conversion between SBGN-ML, SBML, CellDesigner_SBML, GPML uses the MINERVA converter API (https://minerva.pages.uni.lu/doc/api/15.1/converter/). Conversion between json and the other formats uses EscherConverter (https://draeger-lab.github.io/EscherConverter/).

USAGE:

mapFormatConversion (fileNameIn, inputFormat, outputFormat)

INPUTS:

fileNameIn – char, name of the input file; assumed to be in the current directory if a full path is not provided
inputFormat – char, specifying the input format; one of SBGN-ML, SBML, CellDesigner_SBML, GPML
outputFormat – char, specifying the output format; one of SBGN-ML, SBML, CellDesigner_SBML, GPML, json

Example

fileNameIn = ‘iDopa_fol.sbgn’; inputFormat = ‘SBGN-ML’; outputFormat = ‘json’; mapFormatConversion(fileNameIn, inputFormat, outputFormat)

Note

Please cite: Closing the gap between formats for storing layout information in systems biology. David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider. Briefings in Bioinformatics, Volume 21, Issue 4, July 2020, Pages 1249-1260, https://doi.org/10.1093/bib/bbz067 Andreas Draeger, Devesh Khandelwal, Maria Heitmeier, https://github.com/draeger-lab/EscherConverter