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koelling / dnacol

Color DNA/RNA bases in terminal output
MIT License
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Protein coloring #3

Closed lucyforrest closed 7 years ago

lucyforrest commented 7 years ago

Color for proteins too, please! (hydrophobic vs hydrophilic vs charged is most important, if you want a simple scale)

koelling commented 7 years ago

Thank you for your suggestion, I will try to add this in the next version! What kind of file format would these sequences usually come in? FASTA? And is there already a standard color scheme for this that we should use?

lucyforrest commented 7 years ago

Yes, Fasta. You might check jalview and weblogo for some standard color schemes.

Thanks!!! Lucy

=================== Dr. Lucy R Forrest, DPhil NIH-NINDS Porter Neuroscience Building 35 Convent Dr, Room 3D991 Bethesda MD 20892-3761 USA Tel: 301-402-2012 Cell: 301-335-7392 Web: www.forrestlab.org Twitter: @lucyrforrest

From: Nils Koelling notifications@github.com Reply-To: koelling/dnacol reply@reply.github.com Date: Thursday, August 3, 2017 at 1:02 PM To: koelling/dnacol dnacol@noreply.github.com Cc: "Forrest, Lucy (NIH/NINDS) [E]" lucy.forrest@nih.gov, Author author@noreply.github.com Subject: Re: [koelling/dnacol] Protein coloring (#3)

Thank you for your suggestion, I will try to add this in the next version! What kind of file format would these sequences usually come in? FASTA? And is there already a standard color scheme for this that we should use?

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gringer commented 7 years ago

I've been using the RasMol colour scheme for my protein sequences:

http://life.nthu.edu.tw/~fmhsu/rasframe/COLORS.HTM

koelling commented 7 years ago

Made a first test version of this - would this be something like what you are looking for?

screen shot 2017-08-25 at 15 38 14

lucyforrest commented 7 years ago

Yeah! Cool!

From: Nils Koelling notifications@github.com Reply-To: koelling/dnacol reply@reply.github.com Date: Friday, August 25, 2017 at 10:39 AM To: koelling/dnacol dnacol@noreply.github.com Cc: "Forrest, Lucy (NIH/NINDS) [E]" lucy.forrest@nih.gov, Author author@noreply.github.com Subject: Re: [koelling/dnacol] Protein coloring (#3)

Made a first test version of this - would this be something like what you are looking for?

[creen shot 2017-08-25 at 15 38 14]https://user-images.githubusercontent.com/369559/29718686-80f4bcfa-89ab-11e7-953e-90c35506898e.png

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/koelling/dnacol/issues/3#issuecomment-324939933, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AV57oPH2tkMr8sCKYpzH3gEkYfFi0uzPks5sbtybgaJpZM4OsmjG.

koelling commented 7 years ago

I have added a new pcol command to version 0.4, which is now on pip! You should be able to upgrade using pip install dnacol --upgrade.