Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Adding draw png subcommand #11

Merged
merged 4 commits into from
Apr 13, 2022
Merged

Conversation

lucblassel
Copy link
Contributor

Goal

it draws an input alignment to a png file, one sequence per line and one pixel per character.
This can be useful to quickly visualize a large alignment where other viewers like bioJS or seaview might struggle.

Color choice

There are 2 different color schemes:

  • Nucleotides: comes from the bioSyntax paper
  • Amino Acids: adapetd from the Shapely colour scheme found here

The color scheme is selected from the alignment alphabet with the bioSyntax scheme being preferred in case of alphabet ambiguity.

remarks

I chose png as the command name but it might make sense to let the user decide the output format and rename the command to something like image.

@fredericlemoine
Copy link
Collaborator

Thanks @lucblassel !

@fredericlemoine fredericlemoine merged commit bd2fbd4 into evolbioinfo:dev Apr 13, 2022
@lucblassel lucblassel deleted the png branch April 13, 2022 16:34
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants