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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)
63 lines
3.2 KiB
Markdown
63 lines
3.2 KiB
Markdown
# `obiconvert`: Semantic Overview of Public Functionalities
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The `obiconvert` package provides a robust, CLI-driven framework for converting and managing biological sequence data within the OBITools4 ecosystem. It enables format-agnostic input parsing, standardized output generation (FASTA/FASTQ/JSON), and configurable preprocessing—while preserving metadata semantics.
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## Input Handling
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- **`ExpandListOfFiles(check_ext bool, filenames ...string) []string`**
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Expands file paths into a deduplicated list of eligible files. Supports local directories, symlinks (resolved), and remote URLs (`http(s)://`, `ftp://`).
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When `check_ext=true`, filters files by extension: `.fasta[.gz]`, `.fastq[.fq][.gz]`, `.seq[.gz]`, `.gb[| gbff | dat ][.gz]`, and `.ecopcr[.gz]`.
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- **`CLIReadBioSequences(filenames ...string) obiiter.IBioSequence`**
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Returns a lazy, streaming iterator over biological sequences from files or stdin. Automatically selects parsing strategy based on CLI flags:
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- JSON-style (`--input-json-header`)
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- OBI-compliant headers (`--input-OBI-header`, `--input-obi`)
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- Heuristic auto-detection (default).
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Configurable via CLI options:
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- Parallel workers (`nworkers ≥ 2`)
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- Batch size and memory limits
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- `U→T` conversion for RNA (`--u-to-t`)
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- Skip empty sequences (`--skip-empty`)
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Handles:
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- Single/multiple files (with batched parallel reading)
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- Paired-end input via `--paired-with`
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- Fallback readers: FASTA, FASTQ, GenBank/EMBL, ecoPCR output, CSV
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- **`OpenSequenceDataErrorMessage(args ...string, err error)`**
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Formats and logs user-friendly errors for input failures (stdin-only / single-file / multi-file), then exits with status `1`.
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## Output Handling
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- **`CLIWriteBioSequences(iter obiiter.IBioSequence, filenames ...string)`**
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Writes sequences from an `IBioSequence` iterator to stdout or files, based on CLI options:
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- **Format**: FASTQ (if quality scores present), FASTA, JSON (default), or generic sequence.
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- **Header style**: Configured via `CLIOutputFastHeaderFormat()` → `"json"` or `"obi"`.
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- **Compression**: Optional gzip (`--gzip`).
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- **Paired-end output**: Automatically splits into `_R1`, `_R2` files via `BuildPairedFileNames`.
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- **Parallelism**: Uses configurable workers (`WriteParallelWorkers()`).
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- **`BuildPairedFileNames(filename string) (string, string)`**
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Generates paired-end filenames: `sample.fastq → sample_R1.fastq`, `sample_R2.fastq`.
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## Configuration & Integration
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- **`OptionSet(allow_paired bool)`**
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Centralized CLI option setter. Enables modular setup for paired-end support and shared flags.
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- **Taxonomy Integration**:
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Supports loading taxonomy via `obioptions.LoadTaxonomyOptionSet`.
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- **Progress Reporting**:
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Displays a progress bar unless stderr is redirected or stdout pipes to another process.
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## Design Principles
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✅ Lazy evaluation via iterators for memory efficiency
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✅ Automatic format inference and parallel I/O scaling
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✅ Symlink resolution, recursive globbing with extension filtering
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✅ CLI-integrated configuration (header parsing mode, workers, batch size)
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All functionality is exposed through public functions and designed for composability with `obiformats`, `obiiter`, and `obidefault`.
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