generate-names.pl
Name Searching and Autocompletion
The JBrowse search box auto-completes the names of features and reference sequences that are typed into it. After loading all feature and reference sequence data into a JBrowse instance (with prepare-refseqs.pl, flatfile-to-json.pl, etc.), generate-names.pl must be run to build the indexes used for name searching and autocompletion.
Autocompletion Configuration
Several settings are available to customize the behavior of autocompletion. Most users will not need to configure any of these variables.
| Option | Value |
|---|---|
autocomplete→stopPrefixes | Array of word-prefixes for which autocomplete will be disabled. For example, a value of ['foo'] will prevent autocompletion when the user as typed 'f', 'fo', or 'foo', but autocompletion will resume when the user types any additional characters. |
autocomplete→resultLimit | Maximum number of autocompletion results to display. Defaults to 15. |
autocomplete→tooManyMatchesMessage | Message displayed in the autocompletion dropdown when more than autocomplete→resultLimit matches are displayed. Defaults to 'too many matches to display'. |
generate-names.pl
This script builds indexes of features by label (the visible name below a feature in JBrowse) and/or by alias (a secondary name that is not visible in the web browser, but may be present in the JSON used by JBrowse).
To search for a term, type it in the autocompleting text box at the top of the JBrowse window.
Basic syntax:
bin/generate-names.pl [options]
Note that generate-names.pl does not require any arguments. However, some options are available:
| Option | Value |
|---|---|
| --out | A path to the output directory (default is 'data/' in the current directory). |
| --verbose | This setting causes information about the division of nodes into chunks to be printed to the screen. |
| --hashBits | Sets the number of bits, or the filename length. If you get the error "Error reading from name store", try manually setting --hashBits to 16. |
| --completionLimit | Defines the number of letters used in the auto-completion. Example: --completionLimit 0 to disable autocompletion. |
| --incremental | Incrementally index new tracks. Fixed in version 1.11.6. |
| --tracks | A comma separated list of tracks to index. Can be combined with other options such as --incremental and --completionLimit to only provide autocompletion on certain tracks. |
| --workdir | Output the temporary files for names generation to a specific directory. Fixed in 1.11.6. |
View bin/generate-names.pl --help for more options. Note that if you are getting 404 errors for names/root.json then JBrowse is falling back to the legacy names store (and failing) so it is likely that you need to retry generate-names.
Indexing custom fields in GFF
By default, the Name, ID, and Alias fields, for all feature types (gene, mRNA, CDs, exon, etc.), are indexed by generate-names.pl
If you want to index more or different custom fields, you can run flatfile-to-json.pl (not generate-names.pl!) with --nameAttributes "name,id,alias,gene_id" for example, then it will also load the "gene_id" field as a name, and then you can re-run generate-names.pl and the gene_id can be searched for.
Also note that if you have a GFF3Tabix track (which is not loaded via flatfile-to-json.pl) then you can add a nameAttributes=name,id,alias,gene_id to the config for example.
If you have a GFF3Tabix track, you can also select the feature types that you want to index, by adding indexedFeatures=gene,mRNA to the config for example. Other feature types will not be indexed.