bird-tool-utils 0.6.0

Python utilities used as part of the bird suite of bioinformatic tools

A set of Python utilities used as part of the bird suite of bioinformatic tools, developed by the Woodcroft research lab at the Centre for Microbiome Research at the Queensland University of Technology. The classes and functions inside are often heavily opinionated to reduce downstream coding effort and to standardise UI. They may change without warning.

Current utilities:

• SeqReader().readf[aq] - pure python generator function for reading FASTA / FASTQ files
• BirdArgparser - opinionated way of presenting help messages - default help prints examples with colour, --full-help shows a man page. --full-help-roff can be used to generate HTML versions. Logging arguments are batteries included. Subcommands that should run without additional arguments can be created with allow_no_args=True.
• table_roff for generating ROFF format tables for use with BirdArgparser
• in_working_directory and in_tempdir are context functions for temporary switching to a directory
• iterable_chunks provides chunking for iterables