Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
1.8 KiB
obiutils — Universal File I/O with Transparent Compression Support
The xopen-based package in the obiutils module provides a unified interface for reading and writing files, streams, HTTP resources, or command outputs—transparently handling multiple compression formats: gzip, xz, zstd, and bzip2.
Key Functionalities
-
Ropen(f string)
Opens a file, stdin ("-"), HTTP(S) URL, or shell command (e.g.,"|gzip -dc file.gz") for buffered reading, auto-detecting compression via magic bytes. -
Wopen(f string)/WopenFile(...)
Opens a file or stdout ("-") for buffered writing, automatically compressing output based on extension (.gz,.xz,.zst,.bz2). -
Compression Detection
Functions likeIsGzip(),IsXz(),IsZst(), andIsBzip2()inspect the first bytes of a buffered reader to infer format. -
Path Utilities
ExpandUser(path)expands POSIX-style paths (~,~/path) to absolute ones.Exists(path)checks file existence after user expansion.
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Error Handling
Defines semantic errors:ErrNoContent,ErrDirNotSupported. -
Buffered IO
All readers/writers use a default buffer size of65,536bytes for performance. -
Resource Management
Close()methods ensure proper cleanup of underlying readers/writers and compression streams.
Supported Sources & Formats
| Source | Format(s) |
|---|---|
| Local files | plain, .gz, .xz, .zst, .bz2 |
Stdin ("-") |
auto-detected |
| HTTP(S) URLs | transparent decompression on stream read |
| Pipe commands (`" | cmd"`) |
This abstraction simplifies bioinformatics or data-processing pipelines where input sources vary widely, and compression is common.