core.lib.pgsexceptions

This module defines a custom PGS exception hierarchy.

This module overrides sys.excepthook. Uncaught exceptions are intercepted, and sys.exit() is called with a custom code. This can be helpful to debug problems in other applications, because there are relatively few failure states.

The hierarchy:

• BasePGSException

  • MatchError

    • DuplicateMatchError

    • MatchRateError

    • ZeroMatchesError

    • MatchValueError

  • CombineError

    • BuildError

    • ScoreFormatError

    • LiftoverError

  • CatalogError

    • ScoreDownloadError

    • ScoreChecksumError

    • QueryError

    • InvalidAccessionError

  • SamplesheetError

    • GenomesNotFound

    • SamplesheetFormatError

Exceptions

BasePGSException	The base class from which all PGS errors must inherit.
BuildError	Raised when there's a problem with a scoring file genome build.
CatalogError	The base class for errors when querying or downloading from the PGS Catalog
CombineError	The base class for errors that are raised when combining scorefiles
DuplicateMatchError	Raised when a matched variant has been duplicated, so that a variant with the same ID
EffectTypeError	Raised when non-supported effect types are present
GenomesNotFound	Raised when FileNotFound
InvalidAccessionError	Raised when an invalid term is used to query the Catalog
LiftoverError	Raised when liftover has failed to convert genomic coordinates well
MatchError	The base class for errors that are raised during variant matching
MatchRateError	Raised when match rate is below match threshold for one or more scoring files
MatchValueError	Raised when a match function receives inappropriate values.
QueryError	Raised when the Catalog API doesn't return a valid response
SamplesheetError	The base class for errors related to samplesheet parsing
SamplesheetFormatError	Raised when a samplesheet is badly formatted
ScoreChecksumError	Raised when a scoring file fails checksum validation
ScoreDownloadError	Raised when a scoring file can't be downloaded
ScoreFormatError	Raised when there's a problem with a scoring file.
ZeroMatchesError	Raised when zero matches are found for one or more scoring files.

Classes

ExceptionExitCodeMap

A read only map to get exit codes for custom exceptions

Functions

handle_uncaught_exception(→ None)

Intercept BasePGSExceptions and trigger sys.exit with a custom code

Module Contents

exception core.lib.pgsexceptions.BasePGSException(message: str)

The base class from which all PGS errors must inherit. The purpose of this class is to simplify finding PGS exceptions and exiting python with a matching custom exit code.

exception core.lib.pgsexceptions.BuildError(message: str)

Raised when there’s a problem with a scoring file genome build.

exception core.lib.pgsexceptions.CatalogError(message: str)

The base class for errors when querying or downloading from the PGS Catalog

exception core.lib.pgsexceptions.CombineError(message: str)

The base class for errors that are raised when combining scorefiles

exception core.lib.pgsexceptions.DuplicateMatchError(message: str)

Raised when a matched variant has been duplicated, so that a variant with the same ID would be split across two rows in an output scoring file.

exception core.lib.pgsexceptions.EffectTypeError(message: str)

Raised when non-supported effect types are present

exception core.lib.pgsexceptions.GenomesNotFound(message: str)

Raised when FileNotFound

exception core.lib.pgsexceptions.InvalidAccessionError(message: str)

Raised when an invalid term is used to query the Catalog

exception core.lib.pgsexceptions.LiftoverError(message: str)

Raised when liftover has failed to convert genomic coordinates well

exception core.lib.pgsexceptions.MatchError(message: str)

The base class for errors that are raised during variant matching

exception core.lib.pgsexceptions.MatchRateError(message: str)

Raised when match rate is below match threshold for one or more scoring files

exception core.lib.pgsexceptions.MatchValueError(message: str)

Raised when a match function receives inappropriate values.

e.g., Multiple chromosomes detected in variant data but data is split per-chromosome

exception core.lib.pgsexceptions.QueryError(message: str)

Raised when the Catalog API doesn’t return a valid response

exception core.lib.pgsexceptions.SamplesheetError(message: str)

The base class for errors related to samplesheet parsing

exception core.lib.pgsexceptions.SamplesheetFormatError(message: str)

Raised when a samplesheet is badly formatted

exception core.lib.pgsexceptions.ScoreChecksumError(message: str)

Raised when a scoring file fails checksum validation

exception core.lib.pgsexceptions.ScoreDownloadError(message: str)

Raised when a scoring file can’t be downloaded

exception core.lib.pgsexceptions.ScoreFormatError(message: str)

Raised when there’s a problem with a scoring file.

exception core.lib.pgsexceptions.ZeroMatchesError(message: str)

Raised when zero matches are found for one or more scoring files.

Distinct from MatchRateError because it’s very common, and caused by bad input data or parameters.

class core.lib.pgsexceptions.ExceptionExitCodeMap

A read only map to get exit codes for custom exceptions

code_map

core.lib.pgsexceptions.handle_uncaught_exception(exctype: type[BaseException], value: BaseException, trace: types.TracebackType | None) → None

Intercept BasePGSExceptions and trigger sys.exit with a custom code