ONEcode is a powerful general data representation framework with a growing collection of associated software. It was originally designed for genomic data in the context of the Vertebrate Genomes Project (VGP).
Data is represented in a very simple ASCII file format that is easy for both humans and
programs to read and interpret. Moreover, there is a corresponding compressed and indexed binary
version for each ASCII file so that production tools built with the
ONEcode library ONElib are very efficient in time and the
size of the data files they manipulate. All fields are strongly typed
and a specific collection of data types constituting a schema that
is normaly encoded at the top of the file, itself in ONEcode format.
A generic viewer ONEview allows one to view ascii and binary files,
and convert between them, also supporting viewing of a subset of
objects in the file. Another core tool ONEstat can provide various
checks including validating files against a given schema in a separate file.
To make the library and command line tools just type make in this top level directory:
make
make install // copies executables to ~/bin
To see a simple annotated ONEcode file and some example usage:
cat TEST/small.seq
make test
The package has no dependencies on other software.
The .md files contain documentation, ONElib.c and
ONElib.h contain the C code library for developers, and
ONEview.c and ONEstat.c encode their respective programs.
The subdirectory SEQUENCE_UTILITIES contains a set of sequence utilities to interconvert between (compressed) fasta/fastq, ONEcode, and BAM/SAM, report statistics, and flexibly extract sequences. It contains its own README.md file.
The documents describing the framework, generic tools, and development library are as follows:
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Framework Description: a description of ONEcode schemas and the data representation framework.
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Generic Tools: the man pages for the generic ONEcode command line tools.
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Library Interface: a standard C library interface for ONEcode developers.
In addition, specific technical documentation can be found within
individual source files, in particular ONElib.h.
Authors: Richard Durbin & Gene Myers
Date: October 2022
Updated: July 2024