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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

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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
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