Definitions¶

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 ‘_’.
OUTPUTS: 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.

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 ‘;’

getRegisteredDatabases()[source]¶

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

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