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author cpt
date Mon, 05 Jun 2023 02:45:31 +0000
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1 # Code organization
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3 This document walks you trough the Geneblocks code. Please request changes if anything is unclear.
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5 - **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...)
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7 - **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.
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9 - **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*).
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11 - **compute_features_levels.py** implements the algorithm for deciding the levels on which the different features (and annotations) are drawn
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13 - **biotools.py** implements generic biology-related methods (reverse_complement, annotation of Biopython records, etc.)