obitools4/autodoc/docmd/pkg/obitools/obicsv/sequence.md

CSV Export Functionality in obicsv Package

The obicsv package provides utilities to convert biological sequence data into structured CSV format. It supports flexible, configurable output through an Options interface.

Core Functions

• CSVSequenceHeader(opt Options):
  Constructs a CSV header row based on enabled options (e.g., id, count, taxid, definition). Additional user-defined attributes are appended, followed by optional sequence and qualities.

• CSVBatchFromSequences(batch BioSequenceBatch, opt Options):
  Converts a batch of biological sequences into CSV records. Each sequence is processed according to the active options:

  • Sequence ID, count, taxonomic identifier (from Taxon() or fallback to raw taxid), and definition.
  • Custom attributes retrieved via GetAttribute(key); missing values replaced by a configurable NA value.
  • Nucleotide sequence (as string) and quality scores (converted to ASCII Phred+shifted format or NA if absent).

• NewCSVSequenceIterator(iter IBioSequence, options ...WithOption):
  Wraps a sequence iterator (IBioSequence) to produce an asynchronous CSV record stream:

  • Optionally auto-detects and includes all sequence attributes (CSVAutoColumn).
  • Launches parallel workers to process batches concurrently.
  • Uses a producer-consumer pattern: one goroutine drives iteration, others write CSV records.

Key Features

• Configurable output columns via option flags (e.g., CSVId(), CSVTaxon()).
• Support for quality scores in standard FASTQ ASCII encoding.
• NA value handling: missing fields replaced with a user-defined placeholder (e.g., ".").
• Parallelization: scalable CSV generation using multiple goroutines.