Closed annahake closed 2 years ago
I found the issue. Now it treats the upper case amino acids the same as the lower case amino acids and therefore takes the first matching color scheme. Is there a way to circumvent that behaviour? In my case, I want to be able to discriminate the amino acid based on other characteristics and display the color accordingly.
The color scheme does not respect case. These seems to be a bug, which I have fixed on this branch: https://github.com/WebLogo/weblogo/tree/139-color-option
However, I will have to think about this change a bit before updating the master branch to make sure I'm not about to break something.
@kalekundert Do you have any insight on this issue? The weblogo colorscheme does not respect case, which seems to have been a feature you added a long while ago when you contributed an update to weblogo's colors. If I make the colorscheme case sensitive, does that break anything important?
I think I just thought that case-insensitive was more convenient, e.g. if the default color scheme specifies "DEKRH" as charged, it seems like it would be surprising if only upper-case sequences were highlighted correctly. But I don't think anything important would break if you change it back.
Thanks for the feedback Kale.
Fixed and released. You should be able to update weblogo and get your logo working.
Thanks Gavin and Kale for the fast reply and fix! Do you know if by updating the conda weblogo package, the newest version will be available or do I have to wait until a newer conda release is available?
That's a good question. I don't actually know how long it takes conda to update. But you can install the latest weblogo with pip install weblogo --upgrade
. Then run weblogo --version
to make sure the version is correct, 3.7.10
Hi,
I have previously used weblogo as a command line version with a custom color scheme:
weblogo --format PNG --size large < alignment.fasta -o logo.png --alphabet 'AaRrNnDdCcEeQqGgHhIiLlKkMmFfPpSsTtWwYyVv*#' --composition equiprobable -X YES --errorbars NO --scale-width NO --resolution 800 -P "" -Y NO --color 'blue' 'ARNDCEQGHILKMFPSTWYV*' 'positive' --color 'orange' 'arndceqghilkmfpstwyv#' 'negative'
Now the tool takes only the first color option and disregards the other option. Could you help me on that?
Thank you in advance!
Anna