BaseFileSet file format

[Nicklas Nordborg]

The BaseFileSet (BFS) file format is a new file format that is primarily intended to be used for passing data between BASE and external plug-ins. The intention is that it should complement the existing BASEfile format, which is sometimes hard to parse by external programs (for example R).

A secondary objective is that the BFS format should be re-usable in other use cases.

The main idea is to use multiple files:

• A parameter/metadata file that contains information about what kind of data that is found in the other files.
• Annotation files that contains additional information about various items, such as reporter, assays, etc.
• One or more data files that contains the actual data.

The parameter/metadata file is structured in section with key/value pairs. The annotation files are simple tab-separated tables with configurable number of columns with varying data types. The data files are plain-matrix data files with no row or column headers.

This ticket is about documenting the file format for the various file types, generically and specifically for the plug-in execution use case. Working drafts should be attached to this ticket. The final BFS file format should be documented in the docbook documentation.

[Nicklas Nordborg]

Generic specification of various file types in BFS

[Nicklas Nordborg]

Specification for BFS with spotdata that is imported to BASE

[Nicklas Nordborg]

Specification for BFS with spotdata that is exported from BASE