vampire.anno.tl.motif_msa

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vampire.anno.tl.motif_msa#

vampire.anno.tl.motif_msa(adata, reference=None, *, store_key='motif_msa', match_score=2, mismatch_penalty=-3, gap_open_penalty=-5, gap_extend_penalty=-1)[source]#

Align motif sequences using progressive MSA or pairwise reference alignment.

Parameters:

  • adata (AnnData) – Annotated data with var["motif"] containing motif sequences.

  • reference (str | int | None) – Reference motif. If None, performs a progressive MSA of all motifs. If an int or str, performs pairwise alignments of each motif against the specified reference.

  • store_key (str) – Key under which results are stored in adata.uns.

  • match_score (int) – Match score for alignment.

  • mismatch_penalty (int) – Mismatch penalty for alignment.

  • gap_open_penalty (int) – Gap open penalty.

  • gap_extend_penalty (int) – Gap extension penalty.

Returns:

The updated AnnData with alignment results in uns.

Return type:

AnnData

Examples

>>> import vampire as vp
>>> adata = vp.datasets.wdr7_hprc()
>>> vp.anno.tl.motif_msa(adata)
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