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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)
18 lines
1.5 KiB
Markdown
18 lines
1.5 KiB
Markdown
# EMBL Format Parser for OBITools4
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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:
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- **Entry Boundary Detection**: `EndOfLastFlatFileEntry()` identifies the end of EMBL entries using the signature terminator pattern `//` (with optional CR/LF), enabling chunked file processing.
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- **Two Parsing Modes**:
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- `EmblChunkParser()`: Line-scanning parser for buffered I/O (`io.Reader`).
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- `EmblChunkParserRope()`: Direct rope-based parser for zero-copy processing of large files.
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- **Configurable Options**:
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- `withFeatureTable`: Includes EMBL feature table (`FH`/`FT`) lines.
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- `UtoT`: Converts RNA uracil (`u/U`) to DNA thymine (`t/T`).
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- **Metadata Extraction**: Captures `ID`, `OS` (scientific name), `DE` (description), and taxonomic ID (`/db_xref="taxon:..."`) into sequence annotations.
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- **Sequence Handling**: Parses multi-line EMBL sequences (10-bases-per-group, with position numbers), skipping digits and whitespace.
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- **Parallel Processing**: `ReadEMBL()`/`ReadEMBLFromFile()` support concurrent parsing via worker goroutines, streaming results as `BioSequenceBatch` objects.
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- **Integration**: Outputs are compatible with OBITools4’s iterator framework (`obiiter.IBioSequence`) and sequence type `obiseq.BioSequence`.
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Designed for scalability, the module handles large EMBL files efficiently—ideal for metagenomic or biodiversity data pipelines.
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