• Login
Community
  • Login

[New Plugin] Biotools

Scheduled Pinned Locked Moved Notepad++ & Plugin Development
7 Posts 4 Posters 730 Views
Loading More Posts
  • Oldest to Newest
  • Newest to Oldest
  • Most Votes
Reply
  • Reply as topic
Log in to reply
This topic has been deleted. Only users with topic management privileges can see it.
  • A
    AlexWeinreb
    last edited by AlexWeinreb Nov 26, 2023, 10:14 PM Nov 26, 2023, 9:54 PM

    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!

    T M 2 Replies Last reply Nov 26, 2023, 10:01 PM Reply Quote 5
    • T
      Terry R @AlexWeinreb
      last edited by Nov 26, 2023, 10:01 PM

      @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

      A 1 Reply Last reply Nov 26, 2023, 10:15 PM Reply Quote 2
      • A
        AlexWeinreb @Terry R
        last edited by Nov 26, 2023, 10:15 PM

        @Terry-R Thank you! Updated my post.

        1 Reply Last reply Reply Quote 1
        • M
          Michael Vincent @AlexWeinreb
          last edited by Nov 27, 2023, 3:24 AM

          @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.

          A 1 Reply Last reply Nov 27, 2023, 5:55 PM Reply Quote 5
          • A
            AlexWeinreb @Michael Vincent
            last edited by Nov 27, 2023, 5:55 PM

            @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!

            A 1 Reply Last reply Nov 27, 2023, 6:07 PM Reply Quote 3
            • A
              Alan Kilborn @AlexWeinreb
              last edited by Nov 27, 2023, 6:07 PM

              @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.

              M 1 Reply Last reply Nov 27, 2023, 6:13 PM Reply Quote 5
              • M
                Michael Vincent @Alan Kilborn
                last edited by Nov 27, 2023, 6:13 PM

                @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.

                1 Reply Last reply Reply Quote 5
                3 out of 7
                • First post
                  3/7
                  Last post
                The Community of users of the Notepad++ text editor.
                Powered by NodeBB | Contributors