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32 lines
2.1 KiB
Markdown
32 lines
2.1 KiB
Markdown
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# OBIFormats Package: Semantic Description
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The `obiformats` package provides parsing and formatting utilities for **OBI-compliant FASTA headers**, enabling structured annotation of biological sequences.
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- It supports parsing key-value annotations embedded in sequence definitions (e.g., `key=value;`), including nested dictionaries.
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- Three core parsing functions detect value types:
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- `__match__key__`: Identifies assignment patterns (`Key = ...`).
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- `__obi_header_value_numeric_pattern__`: Matches floats/integers (e.g., `42.0;`).
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- `__obi_header_value_string_pattern__`: Matches quoted strings (e.g., `'example';`).
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- `__match__dict__`: Parses balanced `{...}` blocks, handling nested structures and string delimiters.
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- Boolean detection (`__is_true__/__is_false__`) handles multiple case variants (e.g., `true`, `True`, `TRUE`).
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- The main entry point, **`ParseOBIFeatures(text string, annotations obiseq.Annotation)`,**
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iteratively extracts key-value pairs from a header string and populates an `Annotation` map.
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- Numeric values are stored as integers if they have no fractional part.
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- Dictionary-like strings (e.g., `{'a':1,'b':2}`) are JSON-unmarshalled into typed maps:
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- `*_count` → `map[string]int`,
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- `merged_*` → wrapped in a statistics object (`obiseq.StatsOnValues`).
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- `*_status`/`*_mutation` → `map[string]string`.
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- **`ParseFastSeqOBIHeader(sequence *obiseq.BioSequence)`** applies parsing to a sequence’s definition line, moving annotations into its metadata map and preserving leftover text.
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- **`WriteFastSeqOBIHeade(buffer *bytes.Buffer, sequence)`** serializes annotations back into OBI header format:
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- Strings and booleans use `key=value;`.
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- Maps/dicts are JSON-encoded, then single-quoted for compatibility.
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- Special handling ensures `obiseq.StatsOnValues` are safely marshalled.
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- **`FormatFastSeqOBIHeader(sequence)`** returns the formatted header as a string (zero-copy via `unsafe.String` for performance).
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- Designed to interoperate with the broader OBITools4 ecosystem (`obiseq`, `obiutils`), supporting both human-readable and machine-processable sequence metadata.
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