Exceptions (skbio.core.exception)

This module defines custom exception classes used throughout the core scikit-bio codebase.


FileFormatError Exception raised when a file can not be parsed.
RecordError Exception raised when a record is bad.
FieldError Exception raised when a field within a record is bad.
BiologicalSequenceError General error for biological sequence validation failures.
SequenceCollectionError General error for sequence collection validation failures.
DissimilarityMatrixError General error for dissimilarity matrix validation failures.
DistanceMatrixError General error for distance matrix validation failures.
DissimilarityMatrixFormatError Error for reporting issues in dissimilarity matrix file format.
MissingIDError(missing_id) Error for ID lookup that doesn’t exist in the dissimilarity matrix.
TreeError General tree error
NoLengthError Missing length when expected
DuplicateNodeError Duplicate nodes with identical names
MissingNodeError Expecting a node
NoParentError Missing a parent
FastqParseError Exception raised when a FASTQ formatted file cannot be parsed
GeneticCodeError Base class exception used by the GeneticCode class
GeneticCodeInitError Exception raised by the GeneticCode class upon a bad initialization
InvalidCodonError Exception raised by the GeneticCode class if __getitem__ fails