Python utilities used as part of the bird suite of bioinformatic tools
Project description
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-helpshows a man page.--full-help-roffcan be used to generate HTML versions. Logging arguments are batteries included.table_rofffor generating ROFF format tables for use withBirdArgparserin_working_directoryandin_tempdirare context functions for temporary switching to a directoryiterable_chunksprovides chunking for iterables
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