scvi.data.add_dna_sequence

scvi.data.add_dna_sequence#

scvi.data.add_dna_sequence(adata, seq_len=1344, genome_name='hg38', genome_dir=None, genome_provider=None, install_genome=True, chr_var_key='chr', start_var_key='start', end_var_key='end', sequence_varm_key='dna_sequence', code_varm_key='dna_code')[source]#

Add the DNA sequence to AnnData object.

Uses genomepy under the hood to download the genome.

Parameters:

  • adata (AnnData) – AnnData object with chromatin accessibility data

  • seq_len (int (default: 1344)) – Length of the DNA sequence to extract around the peak center. Defaults to value used in scBasset.

  • genome_name (str (default: 'hg38')) – Name of genome to use, installed with genomepy

  • genome_dir (Path | None (default: None)) – Directory to install genome to, if not already installed

  • genome_provider (str | None (default: None)) – Provider of genome, passed to genomepy

  • install_genome (bool (default: True)) – Install the genome with genomepy. If False, genome_provider is not used, and a genome is loaded with genomepy.Genome(genome_name, genomes_dir=genome_dir)

  • chr_var_key (str (default: 'chr')) – Key in .var for chromosome

  • start_var_key (str (default: 'start')) – Key in .var for start position

  • end_var_key (str (default: 'end')) – Key in .var for end position

  • sequence_varm_key (str (default: 'dna_sequence')) – Key in .varm for the added DNA sequence

  • code_varm_key (str (default: 'dna_code')) – Key in .varm for the added DNA sequence, encoded as integers

Return type:

None

Returns:

None

Adds fields to .varm:

sequence_varm_key: DNA sequence code_varm_key: DNA sequence, encoded as integers

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