Metadata-Version: 1.0
Name: dna-features-viewer
Version: 0.1.3
Summary: Plot features from DNA sequences (e.g. Genbank) with Python
Home-page: UNKNOWN
Author: Zulko
Author-email: UNKNOWN
License: see LICENSE.txt
Description: Dna Features Viewer
        ====================
        
        .. image:: https://travis-ci.org/Edinburgh-Genome-Foundry/DnaFeaturesViewer.svg?branch=master
           :target: https://travis-ci.org/Edinburgh-Genome-Foundry/DnaFeaturesViewer
           :alt: Travis CI build status
        
        
        Dna Features Viewer is a Python library to (wait for it...) visualize DNA
        features, e.g. from GenBank or Gff files, using the plotting library Matplotlib:
        
        .. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/master/examples/by_hand.png
            :align: center
        
        Dna Features Viewer is meant to automatically produce simple and clear plots even
        for sequences with lots of overlapping features and long labels.
        The plots can be output to many different formats (PNG, JPEG, SVG, PDF), e.g.
        for report generation or LIMS interfaces.
        
        
        License
        ---------
        
        Dna Features Viewer is an open-source software originally written at the `Edinburgh Genome Foundry
        <http://edinburgh-genome-foundry.github.io/home.html>`_ by `Zulko <https://github.com/Zulko>`_
        and `released on Github <https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer>`_ under the MIT licence.
        Everyone is welcome to contribute !
        
        Installation
        --------------
        
        If you have PIP installed, just type in a terminal:
        
        .. code:: python
        
            (sudo) pip install dna_features_viewer
        
        Dna Features Viewer can be installed by unzipping the source code in one directory and using this command:
        
        .. code:: python
        
            sudo python setup.py install
        
        
        
        Examples of use
        ----------------
        
        
        Basic plots
        ~~~~~~~~~~~~
        
        In this first example we define features "by hand":
        
        .. code:: python
        
            from dna_features_viewer import GraphicFeature, GraphicRecord
            features=[
                GraphicFeature(start=0, end=20, strand=+1, color="#ffd700",
                               label="Small feature"),
                GraphicFeature(start=20, end=500, strand=+1, color="#ffcccc",
                               label="Gene 1 with a very long name"),
                GraphicFeature(start=400, end=700, strand=-1, color="#cffccc",
                               label="Gene 2"),
                GraphicFeature(start=600, end=900, strand=+1, color="#ccccff",
                               label="Gene 3")
            ]
            record = GraphicRecord(sequence_length=1000, features=features)
            record.plot(fig_width=5)
        
        .. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/master/examples/by_hand.png
            :align: center
        
        
        If we replace `GraphicRecord` by `CircularGraphicRecord` in the code above we obtain
        a circular plot of the construct:
        
        .. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/master/examples/by_hand_circular.png
            :align: center
        
        It is also possible to generate interactive (browser-based) plots by using ``plot_with_bokeh`` instead of ``plot``:
        
        .. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/master/examples/plot_with_bokeh.png
            :align: center
        
        
        Reading the features from a GenBank file
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        DnaFeaturesViewer plays nice with BioPython. As a result it is super easy to plot the content of a Biopython record or directly a GenBank file:
        
        .. code:: python
        
            from dna_features_viewer import BiopythonTranslator
            graphic_record = BiopythonTranslator().translate_record("my_sequence.gb")
            ax, _ = graphic_record.plot(figure_width=10)
        
        .. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/master/examples/from_genbank.png
            :align: center
        
        The class ``BiopythonTranslator`` determines how the genbank information is transformed into graphical features.
        It enables to chose which categories of features to plot, the color of the different features.
        
        Displaying the features along with other plots
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        As it uses Matplotlib, Dna Features Viewer can display the features on top of
        other sequences statistics, such as the local GC content:
        
        .. code:: python
        
            import matplotlib.pyplot as plt
            from dna_features_viewer import BiopythonTranslator
            from Bio import SeqIO
            import numpy as np
        
            fig, (ax1, ax2) = plt.subplots(2, 1, figsize=(8, 4), sharex=True)
        
            # Parse the genbank file, plot annotations
            record = SeqIO.read("example_sequence.gb", "genbank")
            graphic_record = BiopythonTranslator().translate_record(record)
            ax, levels = graphic_record.plot()
            graphic_record.plot(ax=ax1, with_ruler=False)
        
            # Plot the local GC content
            def plot_local_gc_content(record, window_size, ax):
                gc_content = lambda s: 100.0*len([c for c in s if c in "GC"]) / len(s)
                yy = [gc_content(record.seq[i:i+window_size])
                      for i in range(len(record.seq)-window_size)]
                xx = np.arange(len(record.seq)-window_size)+25
                ax.fill_between(xx, yy, alpha=0.3)
                ax.set_ylabel("GC(%)")
        
            plot_local_gc_content(record, window_size=50, ax=ax2)
        
            # Resize the figure
            fig.savefig("with_plot.png")
        
        .. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/master/examples/with_plot.png
            :align: center
        
        Dna Features Viewer is pretty minimal in terms of features but easily extensible since it uses Matplotlib as a backend.
        
Keywords: DNA Sequence Feature Genbank Biopython Matplotlib
Platform: UNKNOWN
