biocantor.exc

Module Contents

exception biocantor.exc.BioCantorException

Bases: Exception

Base exception class for BioCantor.

exception biocantor.exc.InvalidStrandException

Bases: BioCantorException

Raised when an operation is performed on an invalid strand – usually this is when an operation is strand-specific but the provided Strand is Unstranded.

exception biocantor.exc.InvalidPositionException

Bases: BioCantorException

Raised when a position is outside of a valid range for the operation being performed.

exception biocantor.exc.UnsupportedOperationException

Bases: BioCantorException

Raised when an object is being used for a comparison like intersection or union in a way that is unsupported.

exception biocantor.exc.LocationException

Bases: BioCantorException

Raised when a Location constructor is given invalid inputs, such as an unequal number of start/end positions.

exception biocantor.exc.LocationOverlapException

Bases: LocationException

Raised when a Location operation that requires overlap is being performed on Locations that do not overlap.

exception biocantor.exc.EmptyLocationException

Bases: LocationException

Raised when a Location operation that requires a non-empty location is being performed on an EmptyLocation.

exception biocantor.exc.AlphabetError

Bases: BioCantorException

Raised when an operation on an Alphabet is unsupported for the provided Alphabet.

exception biocantor.exc.NoSuchAncestorException

Bases: BioCantorException

Raised when the provided Location or Parent does not have an Ancestor of the specified type.

exception biocantor.exc.ValidationException

Bases: BioCantorException

Raised when object constructors are given invalid inputs that are not LocationExceptions.

exception biocantor.exc.InvalidCDSIntervalError

Bases: ValidationException

Raised when CDS-specific constructor items are invalid.

exception biocantor.exc.EmptySequenceFastaError

Bases: BioCantorException

Raised when FASTA export is attempted on an empty Sequence object.

exception biocantor.exc.NoncodingTranscriptError

Bases: BioCantorException

Raised when operations that require a coding transcript are performed on a non-coding transcript.

exception biocantor.exc.InvalidAnnotationError

Bases: BioCantorException

Raised when Collection objects have invalid arguments.

exception biocantor.exc.InvalidQueryError

Bases: BioCantorException

Raised when range queries on Collection objects are invalid.

exception biocantor.exc.ParentException

Bases: BioCantorException

Generic exception involving Parent objects.

exception biocantor.exc.MismatchedParentException

Bases: ParentException

Raised when operations that require comparing Parent objects are performed with incompatible Parent objects.

exception biocantor.exc.NullParentException

Bases: ParentException

Raised when operations that require a Parent are performed on a parentless Location.

exception biocantor.exc.NullSequenceException

Bases: ParentException

Raised when a Location operation is performed that requires a Sequence and there is no Sequence.

exception biocantor.exc.MismatchedFrameException

Bases: BioCantorException

Raised when the frames list of a CDS does not match the location object.

exception biocantor.exc.DuplicateFeatureError

Bases: BioCantorException

More than one feature GUID was found within a single FeatureIntervalCollection.

exception biocantor.exc.DuplicateTranscriptError

Bases: BioCantorException

More than one transcript GUID was found within a single GeneInterval.