dandelion.base.core.Dandelion.write_vdj

Dandelion.write_vdj(folder='dandelion_data', filename_prefix='all', sequence_key='sequence', clone_key='clone_id')[source]

Writes a Dandelion object to contig-annotation formatted files compatible with multiple platforms (10x Genomics, SeekGene, etc.) so that it can be ingested by other tools.

Produces:

  • {filename_prefix}_contig.fasta : sequences in FASTA format.

  • {filename_prefix}_contig_annotations.csv : contig annotation table with columns matching the 10x / SeekGene contig annotation schema.

Parameters:

  • folder (Path | str, optional) – path to save the output files.

  • filename_prefix (str, optional) – prefix for the output files.

  • sequence_key (str, optional) – column name in .data slot to retrieve and write out in fasta format.

  • clone_key (str, optional) – column name in .data slot for clone id information.

Return type:

None