This function provides the same raw output as tdfread from the statistics toolbox, making sure, that we don’t need that as a prerequesite


[raw] = descFileRead(fileName)


  • fileName – The filename of a tab delimited data file. The first row of the file will be considered to be headers (with spaces being replaced by ‘_’.


  • raw – A struct with one field per header and a char array of all data listed in the column.
getAnnotationFieldName(annotatedField, database, annotationQualifier, qualifierSelection, invertSelection)[source]

Get the cobra field corresponding to the given database for the annotion Qualifier and the given annotated field.


fieldName = getAnnotationFieldName(annotatedField,database,annotationQualifier)


  • annotationField – The base field that is being annotated (e.g. ‘rxn’, ‘model’, ‘comp’, ...)
  • database – The database names of the annotation. (e.g. kegg)
  • annotationQualifier – The annotation qualifier (see for possible qualifiers)

Optional inputs

  • qualifierSelection – Exclude the qualifiers from mappings (default: {}).
  • invertSelection – Invert the qualifierSelection i.e. use only those specified (default: false);


  • fieldNames – The name of the field corresponding to the given annotation.
  • dbIDs – A Cell array with the DB IDs
  • relations – The relations the field has with the db names (for defined fields, this can be a multiple tpes separated by ‘;’

Get all databases registered with along with their pattern and and prefix data.


identifiersDBs = getRegisteredDatabases()
identifiersDBs: A Struct with data on each database registered

with (needs web access). The struct will have the following fields:

  • .name: The name of the database
  • .pattern: A regexp pattern allowed with the db.
  • .prefix: The prefix of the db on