Opened 15 years ago
Closed 15 years ago
#1440 closed task (fixed)
BaseFileSet file format
Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
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Priority: | critical | Milestone: | BASE 2.15 |
Component: | documentation | Version: | |
Keywords: | Cc: |
Description (last modified by )
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)
Change History (7)
comment:1 by , 15 years ago
Owner: | changed from | to
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Status: | new → assigned |
comment:2 by , 15 years ago
Description: | modified (diff) |
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by , 15 years ago
Attachment: | bfs-generic-1.txt added |
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by , 15 years ago
Attachment: | bfs-spotdata-import-1.txt added |
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Specification for BFS with spotdata that is imported to BASE
by , 15 years ago
Attachment: | bfs-spotdata-export-1.txt added |
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Specification for BFS with spotdata that is exported from BASE
comment:3 by , 15 years ago
(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 by , 15 years ago
Resolution: | → fixed |
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Status: | assigned → closed |
(In [5245]) Fixes #1440: BaseFileSet file format
Generic specification of various file types in BFS