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https://github.com/metabarcoding/obitools4.git
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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)
30 lines
1.5 KiB
Markdown
30 lines
1.5 KiB
Markdown
# `obiformats` Package: Sequence Writing Utilities
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This Go package provides utilities for writing biological sequence data to files or standard output in FASTA/FASTQ formats.
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## Core Functionality
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- **`WriteSequence()`**:
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Main dispatcher that detects sequence quality data and writes either FASTQ (if qualities present) or FASTA.
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- Accepts an `IBioSequence` iterator, a writable stream (`io.WriteCloser`), and optional configuration.
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- Preserves iterator state via `PushBack()` to allow chaining.
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- **`WriteSequencesToStdout()`**:
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Convenience wrapper writing sequences to `stdout`. Automatically closes the output stream.
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- **`WriteSequencesToFile()`**:
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Writes sequences to a specified file. Supports:
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- File creation/truncation or append mode (`OptionAppendFile()`).
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- Paired-end output: writes mate pairs to a second file if `OptionSavePaired()` is enabled.
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## Design Highlights
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- **Format-Aware Dispatch**: Automatically selects FASTQ vs. FASTA based on presence of quality scores (`HasQualities()`).
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- **Iterator Preservation**: Ensures non-consumed sequences remain available after write operations.
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- **Error Handling & Logging**: Uses `logrus` for fatal errors during file I/O; returns structured error codes.
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- **Configurable Options**: Extensible via `WithOption` pattern (e.g., append mode, paired-end handling).
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## Integration
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Designed for use within the OBITools4 ecosystem—works with `obiiter.IBioSequence` iterators to support streaming, memory-efficient processing of large sequencing datasets.
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