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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)
23 lines
1.5 KiB
Markdown
23 lines
1.5 KiB
Markdown
# CSVSequenceRecord Function Description
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The `CSVSequenceRecord` function converts a biological sequence object (`*obiseq.BioSequence`) into a slice of strings suitable for CSV output. It dynamically constructs the record based on user-defined options (`opt Options`), enabling flexible column selection.
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## Core Features
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- **Sequence ID**: Includes the sequence identifier if `opt.CSVId()` is enabled.
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- **Abundance Count**: Appends the sequence count (e.g., read depth) if `opt.CSVCount()` is true.
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- **Taxonomic Information**: Adds both NCBI taxid and scientific name (retrieved from attributes or fallback via `opt.CSVNAValue()`).
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- **Definition Line**: Includes the sequence definition/description if requested via `opt.CSVDefinition()`.
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- **Custom Attributes**: Iterates over keys from `opt.CSVKeys()` and appends corresponding attribute values (or NA if missing).
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- **Nucleotide Sequence**: Appends the raw sequence string when `opt.CSVSequence()` is enabled.
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- **Quality Scores**: Converts Phred-quality scores to ASCII characters (using a configurable shift) if available; otherwise inserts NA.
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## Design Highlights
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- Uses `obiutils.InterfaceToString()` for safe type conversion of arbitrary attribute values.
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- Handles missing data consistently via `opt.CSVNAValue()`.
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- Supports both standard and user-defined metadata fields.
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- Adapts quality encoding to common formats (e.g., Sanger/Illumina) via `obidefault.WriteQualitiesShift()`.
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This function enables interoperable, configurable export of sequence data to tabular formats.
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