7.1.2.2. cobramod.error¶

Errors for CobraMod

This module creates special errors for CobraMod. Read each error for their explanation.

7.1.2.2.1. Attributes¶

debug_log

7.1.2.2.2. Exceptions¶

`UserInterruption`	Exception that is used if the input of a user interrupts the program flow.
`NoDelimiter`	Simple Error that should be raised when a string does not include the
`GraphKeyError`	Simple Error that should be raised when a value is missing as key in a
`FoundInPairError`	Simple Error that is raised when the pair of a PairDictionary has already
`NodeAttributeError`	Simple Error that should be raised when a
`WrongParserError`	Simple Error that should be raised if a method cannot handle the parsing.
`WrongDataError`	Simple Error that should be raised if COBRApy object is not the correct
`WrongSyntax`	Simple Error that should be raised if a specific syntax is invalid. For
`PatternNotFound`	Simple error that should be raised when a pattern is not found in a item.
`NoIntersectFound`	Simple error that should be raised when no intersect is found between two
`NoGeneInformation`	Simple error that should be raised when given object has no gene
`SuperpathwayException`	Simple Warning that should be raised if a pathway is identified as a
`UnbalancedReaction`	Simple Error that should be raised if a reaction has wrong mass balance.

7.1.2.2.3. Module Contents¶

cobramod.error.debug_log¶

exception cobramod.error.UserInterruption¶

Bases: Exception

Exception that is used if the input of a user interrupts the program flow.

exception cobramod.error.NoDelimiter(string)¶

Bases: Exception

Simple Error that should be raised when a string does not include the delimiter “|”

Parameters:: string (str)

exception cobramod.error.GraphKeyError¶

Bases: Exception

Simple Error that should be raised when a value is missing as key in a graph

exception cobramod.error.FoundInPairError¶

Bases: Exception

Simple Error that is raised when the pair of a PairDictionary has already given key name.

exception cobramod.error.NodeAttributeError¶

Bases: Exception

Simple Error that should be raised when a cobramod.visualization.Node() cannot identify its type.

exception cobramod.error.WrongParserError¶

Bases: Exception

Simple Error that should be raised if a method cannot handle the parsing.

exception cobramod.error.WrongDataError¶

Bases: Exception

Simple Error that should be raised if COBRApy object is not the correct one.

exception cobramod.error.WrongSyntax¶

Bases: Exception

Simple Error that should be raised if a specific syntax is invalid. For instance, when strings do not have a certain number of items when splitted.

exception cobramod.error.PatternNotFound¶

Bases: Exception

Simple error that should be raised when a pattern is not found in a item. e.g. a substring.

exception cobramod.error.NoIntersectFound¶

Bases: Exception

Simple error that should be raised when no intersect is found between two sets.

exception cobramod.error.NoGeneInformation¶

Bases: Exception

Simple error that should be raised when given object has no gene information in the database.

exception cobramod.error.SuperpathwayException¶

Bases: Exception

Simple Warning that should be raised if a pathway is identified as a Superpathway

exception cobramod.error.UnbalancedReaction(identifier, dict_balance)¶

Bases: Exception

Simple Error that should be raised if a reaction has wrong mass balance.

Parameters:

identifier (str)
dict_balance (str)