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BioJSON

Parsers to wrangle the plethora of biological flatfile formats into standard JSON

Install / Use

/learn @levskaya/BioJSON
About this skill

Quality Score

0/100

Supported Platforms

Universal

README

BioJSON

BioJSON is a collection of rough but functional hacks to pull biological flatfiles kicking and screaming into the world of simple data exchange standards.

It uses pyparsing as the recursive descent parsing engine. Currently only the genbank file parser is present, parsers for BLAST, HMMER, and other formats will be added as needed

Genbank Parser

I've used this to parse entire metazoan genomes, so I believe that it should work on the vast majority of NCBI genbank files.
I've also used it to import genbank style files produced by the dna editing programs Vector NTI and ApE

Currently only the sequence and feature table are mapped to JSON in a nice way as these are the features of primary interest to synthetic biologists hacking sequences.

Related Skills

View on GitHub
GitHub Stars10
CategoryDevelopment
Updated2y ago
Forks1

Languages

Python

Security Score

60/100

Audited on May 20, 2023

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