kraut

make-mpa-table

Merges multiple MetaPhlAn profile files into one wide abundance table. Rows are taxa, columns are samples, and missing taxa are filled with 0.

Syntax

kraut make-mpa-table [OPTIONS] INPUT_FILES...

Arguments

Argument	Type	Description
INPUT_FILES...	PATH	Required. One or more MetaPhlAn profile files.

Options

Option	Short	Type	Description
--output	-o	PATH	Output TSV file (default: stdout).
--level	-l	TEXT	Taxonomic level: k, p, c, o, f, g, s, t, or a full rank name (default: S).
--keep-taxid			Add an NCBI_tax_id column.
--short-names			Use terminal clade names only. At species level, include genus plus species.
--drop-unclassified			Drop the UNCLASSIFIED row.
--normalise			Scale each sample column so retained rows sum to 100.

Rows are sorted by mean abundance across samples in descending order. If --normalise is used, sorting uses the normalised abundances. Sample names are inferred from the input filename with the final extension removed.

Examples

Creating a species-level MetaPhlAn table

kraut make-mpa-table profiles/*_profile.tsv -o metaphlan_species.tsv

Adding taxids and shorter labels

kraut make-mpa-table profiles/*.tsv -l species --keep-taxid --short-names -o metaphlan_species.tsv

Creating a genus table without unclassified abundance

kraut make-mpa-table profiles/*.tsv -l genus --drop-unclassified -o metaphlan_genus.tsv

Dropping unclassified and recalibrating to 100

kraut make-mpa-table profiles/*.tsv --drop-unclassified --normalise -o metaphlan_species.tsv

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