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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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1.2 KiB
Semantic Description of obiformats Package
The obiformats package provides core formatting utilities for biological sequence data in standard FASTX formats (FASTA and FASTQ). It defines two functional types:
BioSequenceFormater: Converts a single biological sequence (*obiseq.BioSequence) into its string representation.BioSequenceBatchFormater: Converts a batch of sequences (obiiter.BioSequenceBatch) into raw bytes, suitable for file or stream output.
Two main constructor functions enable flexible formatting:
BuildFastxSeqFormater(format, header)returns a sequence-level formatter based on the requested format ("fasta"or"fastq"), applying optional header metadata viaFormatHeader.BuildFastxFormater(format, header)builds a batch formatter by composing the sequence-level function over all sequences in an iterator-driven batch, concatenating results with newline separators.
The package supports extensibility and type safety through function composition while integrating logging (via logrus) for critical errors—e.g., unsupported formats trigger a fatal log. It abstracts away low-level I/O, focusing purely on semantic formatting logic, making it ideal for pipeline integration in NGS data processing tools.