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 filesBirdArgparser - 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.table_roff for generating ROFF format tables for use with BirdArgparserin_working_directory and in_tempdir are context functions for temporary switching to a directoryiterable_chunks provides chunking for iterablesFAQs
Python utilities used as part of the bird suite of bioinformatic tools
We found that bird-tool-utils demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 3 open source maintainers collaborating on the project.
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