1 follower Follow

Submitting a genbank file to LIMS

I'm a trying to integrate my Geneious with a sort-of-a-LIMS system. For this, i need to submit genbank files to an api endpoint, so i thought i'd make a plugin for that.

First issue i've run into is the generation a GenBank stream. Looking through the example plugin code, i could find how to export Fasta, which makes sense. I can also see how one could put together all the bits and really write a GB file from scratch. I hope however that there's a more standard way of doing this.

Since Geneious can "natively" export such a format, i was hoping there's a serialization function from maybe a AnnotatedPluginDocument class that i can directly call, but i can't find anything like that.

I've also stumbled over the GenBank submission plugin, which i assume has to do this at some point but since the code for this is not available, that's not of much help.

Happy with any support!

Paul Costea

Please sign in to leave a comment.

1 comment


PluginUtilities.exportDocuments() is the easiest way to to do this:

File tempFile = FileUtilities.createTempFile("temp", ".gb", true);
PluginUtilities.exportDocuments(tempFile, myDocument);
Richard Moir 0 votes
Comment actions Permalink