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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)
28 lines
1.4 KiB
Markdown
28 lines
1.4 KiB
Markdown
# Semantic Description of `obiformats` Package
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The `obiformats` package provides utilities for parsing sequence headers in the OBItools4 framework, supporting two distinct formats:
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- **JSON-based format** (e.g., `{"id":"seq1", ...}`): Detected by a leading `{` character.
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- **Legacy OBI format** (plain text, e.g., `>seq1 description`): Used when no JSON prefix is present.
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## Core Functions
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- **`ParseGuessedFastSeqHeader(sequence *obiseq.BioSequence)`**
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Dynamically routes header parsing based on the first character of the sequence definition:
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- Calls `ParseFastSeqJsonHeader` if JSON-prefixed.
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- Otherwise invokes `ParseFastSeqOBIHeader`.
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- **`IParseFastSeqHeaderBatch(iterator, options...) obiiter.IBioSequence`**
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Applies header parsing to a *batch* of sequences:
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- Takes an iterator over `BioSequence`s.
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- Uses optional configuration (e.g., parallelism, parsing behavior).
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- Wraps the parser in a worker pipeline via `MakeIWorker`, preserving sequence flow.
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## Design Principles
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- **Format agnosticism**: Automatically detects header type.
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- **Iterator-based streaming**: Enables memory-efficient batch processing of large datasets (e.g., FASTQ/FASTA).
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- **Extensibility**: Options pattern (`WithOption`) supports runtime customization.
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This package serves as a header-decoding layer for downstream analysis in metagenomic or metabarcoding workflows.
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