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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
1.8 KiB
Markdown
30 lines
1.8 KiB
Markdown
# EcoPCR File Parser for Biological Sequences
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This Go package (`obiformats`) provides functionality to parse EcoPCR output files—tab-delimited CSV-like files containing amplified sequence data generated by the *EcoPCR* tool (used in metabarcoding pipelines). The parser supports two versions of the format (`v1` and `v2`) and extracts rich biological metadata alongside sequences.
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## Key Features
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- **Version Detection**: Automatically detects EcoPCR file version via the `#@ecopcr-v2` header.
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- **Primer Extraction**: Reads forward and reverse primer sequences from comment lines in the file header.
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- **Mode Inference**: Identifies amplification mode (e.g., `direct`, `inverted`) from header metadata.
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- **Sequence Parsing**: Reads each record as a biological sequence (`obiseq.BioSequence`) with:
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- Name (with deduplication support)
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- Nucleotide/protein sequence
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- Comment field
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- **Structured Annotation**: Populates rich annotations including:
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- Taxonomic hierarchy (taxid, rank, species/genus/family names)
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- Primer matching info (`forward_match`, `reverse_mismatch`)
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- Melting temperatures (if present in v2)
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- Amplicon length and strand orientation
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- **Streaming & Batching**: Returns an iterator (`obiiter.IBioSequence`) for memory-efficient, batched processing of large files.
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- **File Handling**: Provides both `ReadEcoPCR` (from any `io.Reader`) and `ReadEcoPCRFromFile` convenience functions.
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## Implementation Highlights
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- Custom line reader (`__readline__`) for robust header parsing.
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- CSV parser configured with `|` delimiter and comment support (`#`).
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- Deduplication of sequence names using a running count suffix.
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- Concurrent goroutine-based streaming to decouple I/O and processing.
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This module integrates with the broader *OBItools4* ecosystem for high-throughput sequence analysis in environmental DNA studies.
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