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rrwick / Bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
http://rrwick.github.io/Bandage/
GNU General Public License v3.0
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Bandage line command cannot interpret colour scheme from GFA file #95 #96

Closed alvipal closed 2 years ago

alvipal commented 4 years ago

Hi,

When I launch Unicycler, I get a GFA graph that I visualize with Bandage. The colors of the nodes are determined inside the GFA file (sample attached in the image) If I open Bandage via the interface, it interprets the colours perfectly. But it's not the same if I launch it via

Bandage image my_graph.gfa imagen.png --toutline 1 --names --fontsize 8

Which command should I use on the shell to achieve Bandage could to interpret the color specified inside the GFA file?

Screenshoot of the inside of GFA file, which include the specification of the node colours: custom_colours_inside_gfa_file

Bandage GUI capable of interpreting the GFA colours: graph_bandage_GUI

Bandage command is NOT able to interpretate the GFA colours: Bandage image my_graph.gfa imagen.png --toutline 1 --names --fontsize 8 imagen

Which command should I use on the shell to achieve Bandage could to interpret the color specified inside the GFA file?

Thanks a lot in advance!!!

rrwick commented 2 years ago

Using --colour custom option should make Bandage use the colours in the GFA file. This is currently only in the development branch, but I will make a new release with this fix shortly.