Came across this library: GitHub - ggonnella/textformats and paper: TextFormats: Simplifying the definition and parsing of text formats in bioinformatics They define a way to describe a text-based file format (like FASTA, SAM) in YAML / JSON and generate readers, writers and validators based on tha…

Not that I’m aware of - most of the parsers in BioJulia use Automa.jl , which generates state machines from regular expressions.

I don’t know of any Julia package that does this. But I’m also skeptical it will bring any value: If the advantage is to automatically generate parsers from higher-level descriptions, then we have ParserCombinator.jl (which I haven’t tried) for nested formats and Automa.jl for flat formats. If the…

Thank you for your comments @jakobnissen I think there is value in a library of specifications of bio-data-formats in a form that can be used directly to generate parsers. The format they propose does not look terrible (to me), but the library is quite limited at this point. If it can grow to somet…

See also [image] [ANN] PikaParser.jl -- small and fast parser library Package Announcements It has been around half a year since we released the first version of PikaParser.jl , and we’re at 0.5.1 today successfully using it for several local projects * . So I th…

TextFormats parser generator

Specific Domains Biology, Health, and Medicine

jar1 March 5, 2023, 9:31am 6

See also

Topic		Replies	Views
ANN: Automa.jl - a package to compile regular expressions to Julia Community package , announcement	6	2941	February 2, 2017
Writing a parser in Julia General Usage	10	7654	August 30, 2018
Resources for writing a parser/lexer General Usage	6	2142	October 1, 2020
How to parse text between specific characters in Julia? New to Julia	3	398	August 28, 2023
State of the Literature/References Community	21	2615	April 22, 2021

TextFormats parser generator

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