reclass reclassifies nonconvex sequences in a reference package.
usage: reclass [options] -c my.refpkg
| -c | Reference package path. Required. |
| -o | Specify the filename to write to. |
| --out-dir | Specify the directory to write files to. |
| --prefix | Specify a string to be prepended to filenames. |
| --csv | Output the results as csv instead of a padded matrix. |
| -j | The number of processes to run pplacer with. default: 2 |
| -p | Calculate posterior probabilities when doing placements. |
| --placefile | Save the placefile generated by running pplacer to the specified location. |
| -t | If specified, the path to write the suggestion tree to. |
Suggest better classifications of sequences in a reference package.
rppr reclass first looks at all ranks of a reference package, starting at the most specific rank, until it finds the first rank with discordance. Discordant leaves are cut off using the convexify algorithm. The sequences corresponding to the cut leaves are then placed with pplacer against the remaining sequences in the reference package.
The result is a table of the suggested reclassifications of these sequences:
| Column name | Description |
|---|---|
| seq_name | The name of the sequence. |
| old_name | The name of the tax_id this sequence used to have. |
| old_taxid | The actual tax_id this sequence used to have. |
| new_name | The name of the suggested tax_id for this sequence. |
| new_taxid | The actual suggested tax_id. |
| makes_convex | true if reclassifying this sequence with the new tax_id will result in a convex tree, otherwise false. |
| uninformative | true if this sequence sits inside a clade determined to be uninformative, otherwise false. |
| old_median_dist | The median distance from this leaf to the convex subset of leaves classified with the previous tax_id. |
| old_avg_cv | The coefficient of variation of the distances from this leaf to the convex subset of leaves classified with the previous tax_id, multiplied by 100%. [1] |
| new_median_dist | The median distance from this leaf to the convex subset of leaves classified with the suggested tax_id. [2] |
| new_avg_cv | The coefficient of variation of the distances from this leaf to the convex subset of leaves classified with the suggested tax_id, multiplied by 100%. [1] |
| n_with_old | The number of leaves in the original tree which were classified with the previoux tax_id. |
| n_nonconvex | The number of leaves in the original tree classified with the previous tax_id which were also non-convex. |
| [1] | (1, 2) This may be - if there are only zero or one other leaves with that tax_id. |
| [2] | This may be - if there are no other leaves with that tax_id. |
Uninformative clades are determined to be clades containing all of the representatives of exactly two tax_ids which are not found anywhere else in the tree.
The suggestion tree emitted with the -t flag is similar to the discordance tree emitted by rppr convexify; it colors all of the leaves which were cut by the convexify step red, colors all of the edges which are considered uninformative (with the overlap between these two sets colored orange), and relabels the cut sequences to include the name of the suggested new classification. The new label is in the format seq_name -> new_name, using the column names described above.