omicverse.alignment.build_amplicon_anndata

omicverse.alignment.build_amplicon_anndata#

omicverse.alignment.build_amplicon_anndata(otutab_tsv, asv_fasta, sintax_tsv=None, sample_metadata=None, sample_order=None)[source]#

Compose anndata.AnnData from vsearch stepwise outputs.

Parameters:

  • otutab_tsv (str) – Path to the --otutabout TSV from vsearch.usearch_global(). First column = ASV id, remaining columns = sample ids.

  • asv_fasta (str) – Path to the ASV centroid FASTA (output of vsearch.unoise3() or the non-chimera FASTA from vsearch.uchime3_denovo()).

  • sintax_tsv (Optional[str] (default: None)) – Optional path to the vsearch --sintax --tabbedout TSV. When supplied, 7-rank taxonomy columns (domain / phylum / class / order / family / genus / species), the ;-joined taxonomy string and sintax_confidence are written into var.

  • sample_metadata (Optional[DataFrame] (default: None)) – Optional DataFrame indexed by sample id; merged into obs.

  • sample_order (Optional[Sequence[str]] (default: None)) – Optional list of sample ids to enforce row order in obs / X. Defaults to the column order of the otutab TSV.

Returns:

X is a scipy.sparse.csr_matrix of int32 counts (samples × ASVs). Same schema as amplicon_16s_pipeline().

Return type:

anndata.AnnData

Contents