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)
1.6 KiB
obicsv Package: CSV Export Functionality for Biological Sequences
This Go package provides utilities to serialize biological sequence data (e.g., from NGS pipelines) into CSV format.
Core Functions
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CLIWriteSequenceCSV()
Converts an iterator ofIBioSequenceobjects into a CSV-compatible stream. It configures parallelism, batching, and compression using default settings (e.g.,obidefault.ParallelWorkers()), then applies CLI-driven column mappings via helper functions (CLIPrintId(),CLIPrintSequence(), etc.). Returns anICSVRecorditerator. -
CLICSVWriter()
Writes the CSV data either to a file (ifobiconvert.CLIOutPutFileName()≠"-") or to standard output. Handles errors with fatal logging and supports optional terminal consumption of the iterator.
Key Features
- Flexible column selection: Controlled by CLI options (e.g.,
CSVTaxon,CSVKeys), allowing selective export of metadata, sequences, quality scores. - Compression support: Output can be gzip-compressed per
obidefault.CompressOutput(). - Parallel processing: Uses ~¼ of configured workers (min 2) for throughput optimization.
- CLI integration: Leverages existing
obiconvertand CLI abstractions for seamless pipeline usage. - Error resilience: Fails fast on I/O issues with descriptive logs.
Design Notes
Functions follow a functional-iterator pattern, enabling lazy evaluation and streaming. The terminalAction flag determines whether the iterator is consumed immediately (e.g., for final output) or returned for further processing.