Mercurial > repos > cpt > cpt_linear_genome_plot
diff dna_features_viewer/README.md @ 1:e923c686ead9 draft
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
| author | cpt |
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| date | Mon, 05 Jun 2023 02:45:31 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/README.md Mon Jun 05 02:45:31 2023 +0000 @@ -0,0 +1,13 @@ +# Code organization + +This document walks you trough the Geneblocks code. Please request changes if anything is unclear. + +- **GraphicFeature.py** implements a class for defining a *GraphicFeature*, which is an annotation (start, end, strand, label) with graphical properties (color, line width, font family...) + +- **GraphicRecord/** implements the *GraphicRecord* class, which can plot a set of *GraphicFeatures* using Matplotlib or Bokeh. To keep file sizes acceptable, many methods are implemented in separate files (*bokeh_plots.py*, *matplotlib_plots.py*) and added to *GraphicRecord* via class mixins. + +- **CircularGraphicRecord/** implements the *GraphicRecord* class, which inherits from *GraphicRecord* but draws features circularly using custom Matplotlib patches called "arrow-wedge" (defined in file *ArrowWedge.py*). + +- **compute_features_levels.py** implements the algorithm for deciding the levels on which the different features (and annotations) are drawn + +- **biotools.py** implements generic biology-related methods (reverse_complement, annotation of Biopython records, etc.)