[New Plugin] Biotools

AlexWeinreb

As a biologist I occasionally use Notepad++ for DNA sequences, and felt the need for a few additional functions: to get the reverse-complement and translation of a DNA sequence, and to find the next ORF (all three are common operations on sequences).

With no prior experience with C++ my code is objectively terrible, but it appears to work.

I put a release in on Github, along with a README with some more details. Comments and suggestions welcome!

Terry R

@AlexWeinreb
I just upvoted you. You should be able to go and edit your post and enter the link correctly. It’s an issue for new forum members with 0 votes.

Terry

AlexWeinreb

@Terry-R Thank you! Updated my post.

Michael Vincent

@AlexWeinreb said in [New Plugin] Biotools:

First off - congratulations on your first plugin! Thank you for the contribution and welcome to the community.

As a biologist … With no prior experience with C++ my code is objectively terrible, but it appears to work.

Do you use scripting languages like Perl (https://github.com/bioperl) or Python (https://biopython.org/) for Bio work?

If you’re more comfortable with the scripting languages, you could use either Python Script (manually install the Python3 version - do not use the ‘Plugin Admin’ Python2 version) or “Perl Script” to integrate the respective language’s Bioinformatics libraries with Notepad++.

Not that new plugins aren’t welcome. But you say you have no C++ experience and there are already existing packages out there in languages that you may be more comfortable in that could integrate with N++. Just a thought …

Cheers.

AlexWeinreb

@Michael-Vincent Thank you!

Indeed, as I mostly use R (which is somewhat similar to Python), the Python script approach would likely be easier.

Now that I already wrote this plugin and consider it essentially feature-complete, I will probably not start again from scratch, but that would definitely have saved me some headaches!

Alan Kilborn

@AlexWeinreb said in [New Plugin] Biotools:

I will probably not start again from scratch

I don’t think Michael was suggesting THAT! :-)
He meant that for future needs, maybe don’t go about it in a relatively difficult way.
Obviously you didn’t know about scripting with Notepad++, but now that you do, you have another possible tool in the toolbox.

Michael Vincent

@Alan-Kilborn said in [New Plugin] Biotools:

scripting with Notepad++, but now that you do, you have another possible tool in the toolbox.

@AlexWeinreb

As @Alan-Kilborn says - if you think you need / want to add more features to the plugin, since you haven’t gone full bore down the C++ route implementing tons of features and it’s just a first release, now would be the time to take a look at PythonScript and see if that integration would be easier for you to add lots of other bio-tools features from the BioPython library.

Cheers.