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22 lines
1.6 KiB
Markdown
22 lines
1.6 KiB
Markdown
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This Go package `obiformats` provides semantic parsing and serialization utilities for FASTQ/FASTA sequence headers encoded in JSON format, primarily used within the OBITools4 framework.
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- **JSON Parsing Helpers**:
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It defines internal functions (`_parse_json_map_*`, `_parse_json_array_*`) to convert JSON objects/arrays into typed Go maps and slices (`map[string]string`, `[]int`, etc.), using the high-performance [`jsonparser`](https://github.com/buger/jsonparser) library for streaming parsing.
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- **Header Interpretation**:
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`_parse_json_header_` interprets a FASTQ/FASTA header string containing embedded JSON metadata. It extracts and assigns:
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- Core fields (`id`, `definition`, `count`)
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- Specialized OBITools annotations (e.g., `"obiclean_weight"`, `"taxid"` with optional taxonomic ranks)
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- Generic annotations of any JSON type (string, number, bool, array, object), preserving numeric precision where possible.
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- **Sequence Annotation Enrichment**:
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`ParseFastSeqJsonHeader` parses the header of a `BioSequence`, extracting JSON metadata into its annotations map and reconstructing non-JSON text as the new definition.
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- **Serialization Support**:
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`WriteFastSeqJsonHeader` and `FormatFastSeqJsonHeader` serialize sequence annotations back into JSON format, appending them to a buffer or returning as string — enabling round-trip compatibility for annotated sequences.
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- **Error Handling**:
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Uses `log.Fatalf` on parsing failures, ensuring malformed headers fail fast during processing.
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In summary: *structured JSON header ↔ BioSequence annotation mapping*, optimized for metabarcoding workflows.
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