Lower case nucleotides do not get any color

[alejandrogzi]

Hi @moshi4

Thanks for your useful tool. Just wanted to report this:

If a .fa file has the nucleotides in lower case, no color is applied (with the exception of "Identity"):

On the other hand, if you convert them to upper case, color schemes work:

I do not know if this is the desired functionality or a real bug (I personally think that they should be colored either way).

Best,
Alejandro

[moshi4]

Hi @alejandrogzi,

The default setting in pyMSAviz is no color for lowercase letters. If users want to set the color even for lowercase letters, it should be set explicitly with the set_custom_color_scheme() method.

e.g. mv.set_custom_color_scheme(dict(a="lime", t="skyblue", g="salmon", c="orange"))