I am looking for a way to represent functional annotations of genes on GenomeDiagram plots. I have an annotated multi-genbank file and a making plots of the contigs by making a GenomDiagram plot for each one and then piecing them together with ImageMagick's 'montage' command. (see below) Right now I am coloring the ORFs by defining a GenomeDiagram feature based on a string lookup - here is an example:
> if feature.type == "CDS": > if "glycotransferase" in str(feature.qualifiers['product']): > gd_feature_set.add_feature(feature, color="yellow")
What I would like to do is to take advantage of an already existing color-scheme and be able to color all the ORFs by a functional class. In the GenomeDiagram _Color.py sourcefile I notice that there is a nice color scheme based on Artemis. In this scheme ORFs are colored based on whether they are part of a Primary Metabolism, Secondary Metabolism, Chaperones, Regulators, etc.. I am wondering if there as an easyway to map my genes to this or another color scheme.
thanks, zach cp