Post

3 followers Follow
0
Avatar

CSV as Plugin Import

I'm trying to use the Wrapper Plugin Creator to make a plugin for a python program that runs through the command line. The program takes as input a CSV exported from a Geneious BLAST consensus results file. According to one of your help pages, the wrapper can accommodate a program which "Accepts input sequences as files on disk in a format that Geneious Prime can export." This would lead me to believe that CSV can be used as the input type, since Geneious can export such files. However, my only choices are .fasta.gz, .fasta, .fastq, .fastq.gz, .gb, .xml, .meg, .nex, .phy. I have the document type selected as "Multiple Alignment (4+ sequences)", but I did try selecting the other options, none of which seemed to have CSV available as a format. Similarly, I tried the different sequence type options to no avail. I have the plugin type selected as "General Operation", as its function is to take the CSV and parse the information in a particular way, creating a new output file sorted in a way that we need for further analysis. If you could advise as to how to select CSV as the input format, I would greatly appreciate it!

Chow

Please sign in to leave a comment.

5 comments

0
Avatar

Firstly, I apologize for the extremely slow reply! Somehow we overlooked this question until now.

Unfortunately you've run into a limitation in our code which detects which exporters are compatible with the type of documents the wrapper plugin accepts. We've fixed this for our next major release (2021.2) of Geneious Prime. Sorry, but I'm unable to think of a work-around for you in the meantime.

Please let us know if you have any further questions and we'll endeavor to answer more promptly next time!

Matt Kearse 0 votes
Comment actions Permalink
0
Avatar

Hi,

I saw the release notes for 2021.2 mentioning that this was fixed, so I excitedly updated to the beta (Geneious Prime® 2021.2.0, Build 2021-06-15 11:22).  It's still not allowing CSV as an input for wrapper plugins.  I tried creating a brand new plugin and going through all the Plugin Types, but none provided CSV as an option.  Is there a newer build?

Thank you!

Chow 0 votes
Comment actions Permalink
0
Avatar

Thanks for letting us know. It turns out this fix passed through our QA process successfully, but we made a mistake in our release process and this fix wasn't included in 2021.2.0 like it should have been. It will be in the next patch (2021.2.1) which will probably be available in about two weeks.

Sorry for the confusion and thanks again for pointing this out to us.

Matt Kearse 0 votes
Comment actions Permalink
0
Avatar

This is mostly working now but I've come across another issue.  Even if the plugin settings say to Export Full Table for the CSV input, fields will not be exported unless they happened to have been selected the last time a manual export was performed.

For example, I want to export a CSV to a plugin that will use the Bit Score, Description, and Grade.  If I included those fields the last time I manually performed an export outside of the plugin, the plugin will work fine.  If I did not include those fields the last time I manually performed an export outside of the plugin, the plugin will give an error stating that those fields cannot be found, regardless of the plugin settings clearly including those fields.

Chow 0 votes
Comment actions Permalink
0
Avatar

Very sorry about that, and thanks for letting us know. Unfortunately it appears our CSV exporter has a non-standard way of handling options preferences which is causing it to not work properly conjunction with the wrapper plugins. We'll look into fixing it.

In the mean time, the only work-around I can think of would be to write your own CSV exporter using our plugin development API. That would be quite a bit of effort to go to though. Sorry I don't have a better suggestion.

Matt Kearse 0 votes
Comment actions Permalink