BioMate represents a collection of scripts and utility tools for everyday processing of biological data, conveniently gathered into a single Python package.
To check the package information and available sub-commands, you can run biomate --help.
- Blabber - FASTA, FASTQ or plain text sequence generator. It can be used to re-generate a demultiplexed flowcell folder using a sample sheet as input.
- Dirstruct - Extract or create a directory structure. It can be used to simulate nested folder structures for testing purposes.
- Indexer - Indexing tool for FASTA/FASTQ files. It can be used to search for expected indexes and get 'fuzzy' information.
- FastRewind - Convert a demultiplexed folder back into the Illumina NovaSeqXPlus output. It can be used to generate a subset for demultiplex testing.
In addition to the --version option, which prints the current version of the BioMate package, the following options can be provided before any sub-command (e.g. biomate <OPTION> <SUBCOMMAND>), and they will be propagated to the sub-command execution:
--verbose: Increase verbosity of the output by setting the logging level toDEBUG. This will print additional information about the execution of the sub-command.--quiet: Decrease verbosity of the output by setting the logging level toWARNING. This will suppress most of the output, only printing warnings and errors.
Note: By default, the logging level is set to
INFO, which will print general information about the execution of the sub-command, but not the detailed debug information.
Important: In some cases (e.g. when the output will be printed to the standard output), the
--quietoption will be applied automatically to avoid cluttering the output with unnecessary information. In such cases, the logging level will be set toWARNINGregardless of the--verboseor--quietoptions.