Tool: Quick & dirty DNA coordinates in any mac app
2
gravatar for rleach
9 months ago by
rleach90
United States
rleach90 wrote:

I just wrote 3 Automator services on my mac that help me with the debugging of DNA modification scripts I've been writing. Of course, there are other ways to do it. I kinda just did it for fun, really.

Briefly, these services allow you to see where a coordinate is in a sequence or obtain the (sequence and alignment) length of a selected sequence (along with an NT breakdown).

Let me know if you like them or find them useful - or how you deal with finding coordinates in text in random apps.

If you'd like step-by-step instructions on usage & installation, or have any trouble or unexpected behavior, more details can be found in my blog post: Automator Services for finding coordinates in DNA/AA strings.

Here's a direct link to the code:

Rob

tool alignment sequence • 480 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by rleach90

Your link is broken. Also, we recommend that full text posts be made right here, so you don't come across as driving traffic to your personal website.

ADD REPLYlink written 9 months ago by RamRS19k

I fixed the link.

ADD REPLYlink written 9 months ago by genomax59k

Thanks! Was just about to fix it.

ADD REPLYlink written 9 months ago by rleach90

That was a copy-paste-o. I would have typed it out yesterday, but couldn't log in because of an issue with github linked accounts, so I posted initially on seqanswers. This morning, I just copied that post here. Didn't check the link, obviously.

ADD REPLYlink written 9 months ago by rleach90

I was wondering where would be appropriate for this sort of post. But where's "here"? Did you intend to link that?

ADD REPLYlink written 9 months ago by rleach90

You can include the GitHub gist links for your code in the original post. Biostars is able to parse those automatically.

ADD REPLYlink modified 9 months ago • written 9 months ago by genomax59k
1

Oh cool. OK. The instructions and explanation of usage are in the blog post though. There's a cursory explanation in the comments of the files in the gist. Do you think that's enough?

ADD REPLYlink written 9 months ago by rleach90

Looks good to me. You could say "check the blog post linked" for detailed instructions.

ADD REPLYlink written 9 months ago by genomax59k

Just added 3 more services: Select N Nucleotides, Select N Alignment Characters, and Select N Sequence Characters. The first 2 work on nucleotide strings and the third will work on amino-acid or quality strings. There is as yet, no service provided for amino acid alignments.

ADD REPLYlink modified 9 months ago • written 9 months ago by rleach90

Added another service: Reverse Complement. Select sequence, right click, & select Reverse Complement. The RC'd sequence shows up in a dialog, pre-selected for copying.

ADD REPLYlink written 9 months ago by rleach90
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