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
obimatrix Package: Semantic Overview
The obimatrix package provides core functionality for generating and formatting sequence count matrices in the OBITools4 ecosystem.
Core Features
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Matrix Generation: Converts sequence annotations into tabular count matrices (samples × features).
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Flexible Output Formats:
- Matrix mode: Standard rectangular format (rows = sequences, columns = samples).
- Three-column mode (
--three-columns): Long format withsample, sequence ID, and value.
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Configurable Attributes:
- Mapping attribute (default:
"merged_sample") used to group sequences per sample. - Customizable column names for value (
--value-name, default"count") and sample ID (--sample-name, default"sample"). - NA handling: Assigns a placeholder value (default
"0") when the mapping attribute is missing.
- Mapping attribute (default:
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Transpose Control (
--transpose): Allows switching between sequence-centric and sample-centric layouts. -
Strictness Option (
--allow-empty): Controls whether sequences lacking the mapping attribute are excluded (default: strict).
Integration
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Extends command-line interface via
getoptions, aggregating options from:- CSV handling (
obicsv.CSVOptionSet) - Input parsing (
obiconvert.InputOptionSet)
- CSV handling (
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Exposes getter functions (e.g.,
CLIMapAttribute(),CLIOutFormat()), enabling downstream tools to retrieve parsed CLI settings programmatically.
Use Case
Designed for post-processing amplicon sequencing results, transforming annotated reads into quantitative matrices suitable for ecological or bioinformatic analysis (e.g., diversity studies, differential abundance).