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Adding draw png subcommand#11

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fredericlemoine merged 4 commits intoevolbioinfo:devfrom
lucblassel:png
Apr 13, 2022
Merged

Adding draw png subcommand#11
fredericlemoine merged 4 commits intoevolbioinfo:devfrom
lucblassel:png

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@lucblassel
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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
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Thanks @lucblassel !

@fredericlemoine fredericlemoine merged commit bd2fbd4 into evolbioinfo:dev Apr 13, 2022
@lucblassel lucblassel deleted the png branch April 13, 2022 16:34
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