4. Export

The Export command converts the pairwise TSV file to a dissimilarity matrix and (optionally) a newick-format file.

Usage: DBRetina export [OPTIONS]

  Export to dissimilarity matrix and newick format.

  Export a pairwise TSV file to a dissimilarity matrix and (optionally) a
  newick-format file.

Options:
  -p, --pairwise PATH   filtered pairwise TSV file  [required]
  -d, --dist-type TEXT  select from ['min_cont', 'avg_cont', 'max_cont',
                        'ochiai', 'jaccard']  [default: max_cont]
  --newick              Convert the dissimilarity matrix to newick tree format
  -l, --labels TEXT     select from ['ids', 'names']  [default: ids]
  -o TEXT               output prefix  [required]
  --help                Show this message and exit.

4.1 Command arguments

-p, --pairwise PATH the pairwise TSV file [required]

The original or a filtered pairwise TSV file.

-d, --dist-type TEXT select from ['min_cont', 'avg_cont', 'max_cont', 'ochiai', 'jaccard'] [default: max_cont]

The distance metric to be utilized in the similarity matrix.

--newick Convert the similarity matrix to newick tree format

This will convert the similarity matrix to a newick tree format.

-l, --labels TEXT select from ['ids', 'names'] [default: ids]

The labels to be used in all outputs (plots, newick, distance matrix) matrix. The default is the IDs which are the IDs found in the {index_prefix}.namesMap file.

-o TEXT custom output file name prefix

The output files prefix.

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4.2 Output files format

{output_prefix}_distmat.tsv

A labels tab-separated similarity matrix file.

{output_prefix}_distmat.pkl

A labels pickle similarity matrix file in Python pickle format.

{output_prefix}.newick

A newick tree file that can be used in tree visualization tools.

{output_prefix}_clustermap.png

A clustermap plot of the similarity matrix.