Opened 11 years ago

Closed 11 years ago

#1440 closed task (fixed)

BaseFileSet file format

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: BASE 2.15
Component: documentation Version:
Keywords: Cc:

Description (last modified by 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.

Attachments (3)

bfs-generic-1.txt (6.2 KB) - added by Nicklas Nordborg 11 years ago.
Generic specification of various file types in BFS
bfs-spotdata-import-1.txt (7.1 KB) - added by Nicklas Nordborg 11 years ago.
Specification for BFS with spotdata that is imported to BASE
bfs-spotdata-export-1.txt (5.7 KB) - added by Nicklas Nordborg 11 years ago.
Specification for BFS with spotdata that is exported from BASE

Download all attachments as: .zip

Change History (7)

comment:1 Changed 11 years ago by Nicklas Nordborg

Owner: changed from everyone to Nicklas Nordborg
Status: newassigned

comment:2 Changed 11 years ago by Nicklas Nordborg

Description: modified (diff)

Changed 11 years ago by Nicklas Nordborg

Attachment: bfs-generic-1.txt added

Generic specification of various file types in BFS

Changed 11 years ago by Nicklas Nordborg

Attachment: bfs-spotdata-import-1.txt added

Specification for BFS with spotdata that is imported to BASE

Changed 11 years ago by Nicklas Nordborg

Attachment: bfs-spotdata-export-1.txt added

Specification for BFS with spotdata that is exported from BASE

comment:3 Changed 11 years ago by Nicklas Nordborg

(In [5244]) References #1440: BaseFileSet? file format

First section about BFS in general is done. Also added an empty document for documenting the BASEfile format (should be added as a new ticket). Fixed an issue with docbook and alignment of tables.

comment:4 Changed 11 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

(In [5245]) Fixes #1440: BaseFileSet? file format

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