autometa.common package

Subpackages

Submodules

autometa.common.coverage module

autometa.common.exceptions module

# License: GNU Affero General Public License v3 or later # A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.

File containing customized AutometaErrors for more specific exception handling

exception autometa.common.exceptions.AutometaError

Bases: Exception

Base class for Autometa Errors.

exception autometa.common.exceptions.BinningError

Bases: autometa.common.exceptions.AutometaError

BinningError exception class.

Exception called when issues arise during or after the binning process.

This is usually a result of no clusters being recovered.

exception autometa.common.exceptions.ChecksumMismatchError

Bases: autometa.common.exceptions.AutometaError

ChecksumMismatchError exception class

Exception called when checksums do not match.

exception autometa.common.exceptions.DatabaseOutOfSyncError(value)

Bases: autometa.common.exceptions.AutometaError

Raised when NCBI databases nodes.dmp, names.dmp and merged.dmp are out of sync with each other :param AutometaError: Base class for other exceptions :type AutometaError: class

__str__()

Operator overloading to return the text message written while raising the error, rather than the message of __str__ by base exception :returns: Message written alongside raising the exception :rtype: str

exception autometa.common.exceptions.ExternalToolError(cmd, err)

Bases: autometa.common.exceptions.AutometaError

Raised when samtools sort is not executed properly.

Parameters

AutometaError (class) – Base class for other exceptions

exception autometa.common.exceptions.TableFormatError

Bases: autometa.common.exceptions.AutometaError

TableFormatError exception class.

Exception called when Table format is incorrect.

This is usually a result of a table missing the β€˜contig’ column as this is often used as the index.

autometa.common.kmers module

autometa.common.markers module

autometa.common.metagenome module

autometa.common.utilities module

Module contents