obitools4/autodoc/docmd/pkg/obiformats/embl_read.md

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 OBITools4’s 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.