Definitions¶
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descFileRead
(fileName)[source]¶ This function provides the same raw output as tdfread from the statistics toolbox, making sure, that we don’t need that as a prerequesite
Usage
[raw] = descFileRead(fileName)Input
- 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 ‘_’.
Output
- raw – A struct with one field per header and a char array of all data listed in the column.
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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.
Usage
fieldName = getAnnotationFieldName(annotatedField,database,annotationQualifier)Inputs
- 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 http://co.mbine.org/standards/qualifiers for possible qualifiers)
Optional inputs
- qualifierSelection – Exclude the qualifiers from mappings (default: {}).
- invertSelection – Invert the qualifierSelection i.e. use only those specified (default: false);
Outputs
- 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 ‘;’
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getRegisteredDatabases
()[source]¶ Get all databases registered with identifiers.org along with their pattern and and prefix data.
Usage
identifiersDBs = getRegisteredDatabases()- OUPUTS:
- identifiersDBs: A Struct with data on each database registered
with identifiers.org (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 identifiers.org