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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)
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CSVSequenceRecord Function Description
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.
Core Features
- Sequence ID: Includes the sequence identifier if
opt.CSVId()is enabled. - Abundance Count: Appends the sequence count (e.g., read depth) if
opt.CSVCount()is true. - Taxonomic Information: Adds both NCBI taxid and scientific name (retrieved from attributes or fallback via
opt.CSVNAValue()). - Definition Line: Includes the sequence definition/description if requested via
opt.CSVDefinition(). - Custom Attributes: Iterates over keys from
opt.CSVKeys()and appends corresponding attribute values (or NA if missing). - Nucleotide Sequence: Appends the raw sequence string when
opt.CSVSequence()is enabled. - Quality Scores: Converts Phred-quality scores to ASCII characters (using a configurable shift) if available; otherwise inserts NA.
Design Highlights
- Uses
obiutils.InterfaceToString()for safe type conversion of arbitrary attribute values. - Handles missing data consistently via
opt.CSVNAValue(). - Supports both standard and user-defined metadata fields.
- Adapts quality encoding to common formats (e.g., Sanger/Illumina) via
obidefault.WriteQualitiesShift().
This function enables interoperable, configurable export of sequence data to tabular formats.