⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)
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Eric Coissac
2026-04-07 08:36:50 +02:00
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# EMBL Format Parser for OBITools4
This Go package (`obiformats`) provides robust, streaming parsers for the **EMBL nucleotide sequence format**, supporting both standard and rope-based (memory-efficient) parsing. Key features:
- **Entry Boundary Detection**: `EndOfLastFlatFileEntry()` identifies the end of EMBL entries using the signature terminator pattern `//` (with optional CR/LF), enabling chunked file processing.
- **Two Parsing Modes**:
- `EmblChunkParser()`: Line-scanning parser for buffered I/O (`io.Reader`).
- `EmblChunkParserRope()`: Direct rope-based parser for zero-copy processing of large files.
- **Configurable Options**:
- `withFeatureTable`: Includes EMBL feature table (`FH`/`FT`) lines.
- `UtoT`: Converts RNA uracil (`u/U`) to DNA thymine (`t/T`).
- **Metadata Extraction**: Captures `ID`, `OS` (scientific name), `DE` (description), and taxonomic ID (`/db_xref="taxon:..."`) into sequence annotations.
- **Sequence Handling**: Parses multi-line EMBL sequences (10-bases-per-group, with position numbers), skipping digits and whitespace.
- **Parallel Processing**: `ReadEMBL()`/`ReadEMBLFromFile()` support concurrent parsing via worker goroutines, streaming results as `BioSequenceBatch` objects.
- **Integration**: Outputs are compatible with OBITools4s iterator framework (`obiiter.IBioSequence`) and sequence type `obiseq.BioSequence`.
Designed for scalability, the module handles large EMBL files efficiently—ideal for metagenomic or biodiversity data pipelines.