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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)
27 lines
1.8 KiB
Markdown
27 lines
1.8 KiB
Markdown
# FastSeq Reader Module — Semantic Description
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This Go package (`obiformats`) provides high-performance parsing of FASTA/FASTQ files using a C-backed library (`fastseq_read.h`). It enables streaming, batched reading of biological sequences with optional quality scores.
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## Core Features
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- **C-based FASTX parsing**: Leverages `kseq.h` via Go's cgo for efficient, low-level file/stream parsing.
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- **Batched iteration**: Sequences are grouped into configurable batches (`batch_size`) for memory-efficient processing.
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- **Quality score handling**: Supports FASTQ; decodes Phred quality scores using a configurable shift offset (`obidefault.ReadQualitiesShift()`).
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- **Source tracking**: Each sequence carries its origin (filename or `"stdin"`), aiding provenance.
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- **Header parsing hook**: Optional custom header parser (`ParseFastSeqHeader`) allows metadata extraction or transformation.
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- **Full-file batching mode**: When enabled, yields a single batch containing the entire file (useful for small files or global operations).
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- **Stdin & File I/O**: Two entry points:
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- `ReadFastSeqFromFile(filename, ...)` for regular files.
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- `ReadFastSeqFromStdin(...)` to process piped input (e.g., from upstream tools).
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- **Error resilience**: Gracefully handles missing files, with logging (via `logrus`) for debugging.
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- **Async streaming**: Uses goroutines to decouple reading from consumption, enabling concurrent pipelines.
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## Integration
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Built on top of `obitools4`’s core abstractions:
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- `obiiter.IBioSequence`: Iterator interface for biological sequences.
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- `obiseq.BioSequence`: Data model holding name, sequence bytes, comment, and quality.
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- `obiutils`, `obidefault`: Utilities for path handling and defaults.
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Designed for scalability in high-throughput metabarcoding pipelines.
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