autometa.common packageο
Subpackagesο
- autometa.common.external package
- Submodules
- autometa.common.external.bedtools module
- autometa.common.external.bowtie module
- autometa.common.external.diamond module
- autometa.common.external.hmmscan module
- autometa.common.external.hmmsearch module
- autometa.common.external.prodigal module
- autometa.common.external.samtools module
- Module contents
Submodulesο
autometa.common.coverage moduleο
autometa.common.exceptions moduleο
# 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.AutometaErrorο
Bases:
Exception
Base class for Autometa Errors.
- exception autometa.common.exceptions.BinningErrorο
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.ChecksumMismatchErrorο
Bases:
autometa.common.exceptions.AutometaError
ChecksumMismatchError exception class
Exception called when checksums do not match.
- exception autometa.common.exceptions.DatabaseOutOfSyncError(value)ο
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__()ο
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)ο
Bases:
autometa.common.exceptions.AutometaError
Raised when samtools sort is not executed properly.
- Parameters
AutometaError (class) β Base class for other exceptions
- exception autometa.common.exceptions.TableFormatErrorο
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 βcontigβ column as this is often used as the index.