fixed setup.py and will be adding tests

.gitignore

@@ -1,6 +1,5 @@
-src/test.py
-src/biograpy/tests/*.png
-src/biograpy/tests/*.svg
-src/biograpy/tests/*.pdf
-src/biograpy/tests/*.jpg
+tests/*.png
+tests/*.svg
+tests/*.pdf
+tests/*.jpg
 .DS_Store

README.md

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+BioGraPy - Biological Graphical Library in Python
+=================================================
+
+Fork that adds support to plot the tracks below an existing figure, and adds some new features to draw such as text sequence with automatic font size and highlighted text.
+
+```python
+import matplotlib
+import matplotlib.pyplot as plt
+from matplotlib.font_manager import FontProperties
+import numpy as np
+
+import biograpy
+from Bio.SeqFeature import SeqFeature, FeatureLocation
+from Bio.Seq import Seq
+
+
+fig1, ax = plt.subplots(figsize=(10,3), dpi=300)
+
+ax.scatter(x=list(range(0, 1200)), y=np.random.random(1200))
+ax.set_xlim([0,1200])
+ax.set_ylim([0,2])
+
+# We use the package biograpy to create Panel, tracks, and features
+panel = biograpy.Panel(fig1)
+track = biograpy.tracks.BaseTrack()
+
+# Simple feature drawn as a rectangle
+track.add_feature(biograpy.features.Simple(name='Simple1', start = 50, end = 300))
+
+# Gene feature drawn as an arrow
+genefeat = SeqFeature(FeatureLocation(100,500), type='gene', strand=1)
+track.add_feature(biograpy.features.GeneSeqFeature(genefeat, name='GeneSeqFeature1'))
+
+# Simple feature with color
+track.add_feature(biograpy.features.Simple(name='Simple_colored1', start = 500, end = 820, color_by_cm=False, fc='r'))
+
+# Gene feature with color
+track.add_feature(biograpy.features.GeneSeqFeature(genefeat,name='GeneSeqFeature2_colored',fc='r'))
+
+# Very short gene feature (to test the arrow head automatic sizing)
+genefeat = SeqFeature(FeatureLocation(800,810), type='gene', strand=1)
+track.add_feature(biograpy.features.GeneSeqFeature(genefeat, name='GeneSeqFeature_very_short'))
+
+# mRNA with one CDS drawn as a shaded rectangle with an arrow on top
+CDS_feature = SeqFeature(FeatureLocation(180,1000), type='CDS', strand=-1)
+mRNA_feature = SeqFeature(FeatureLocation(180,1100), type='mRNA', strand=-1)
+mRNAandCDSfeat = biograpy.features.CoupledmRNAandCDS(mRNA_feature, CDS_feature,
+                                                     name='CoupledmRNAandCDS1_strandm', ec='k')
+track.add_feature(mRNAandCDSfeat)
+
+# mRNA with CDS, custom color
+CDS_feature = SeqFeature( FeatureLocation(200,600), type='CDS', strand=1)
+mRNA_feature = SeqFeature( FeatureLocation(100,800), type='mRNA', strand=1)
+mRNAandCDSfeat = biograpy.features.CoupledmRNAandCDS(mRNA_feature, CDS_feature,
+                                                     name='CoupledmRNAandCDS1_strandp_colored', ec='r', fc='r')
+track.add_feature(mRNAandCDSfeat)
+
+# Very short mRNA with CDS (to test the arrow head automatic sizing)
+CDS_feature = SeqFeature( FeatureLocation(250,260), type='CDS', strand=1)
+mRNA_feature = SeqFeature( FeatureLocation(220,300), type='mRNA', strand=1)
+mRNAandCDSfeat = biograpy.features.CoupledmRNAandCDS(mRNA_feature, CDS_feature,
+                                                     name='CoupledmRNAandCDS1_very_short')
+track.add_feature(mRNAandCDSfeat)
+
+# Gene feature on minus strand
+geneSeqfeat = SeqFeature( FeatureLocation(900,200), type = 'gene', strand=-1)
+genefeat = biograpy.features.GeneSeqFeature(geneSeqfeat, name='GeneSeqFeature3_strandm')
+track.add_feature(genefeat)
+
+track2 = biograpy.tracks.BaseTrack(biograpy.features.Simple(name='Simple3_track2', start= 0, end = 80))
+
+panel.add_track(track)
+panel.add_track(track2)
+panel._draw_tracks()
+panel.save('biograpy_test1.png')
+```
+
+![example1](/examples/biograpy_test1.png)
+
+```python
+fig1, ax = plt.subplots(figsize=(11,3), dpi=400)
+
+ax.scatter(x=list(range(0, 100)), y=np.random.random(100))
+ax.set_xlim([0,100])
+ax.set_ylim([0,2])
+
+# Create panel and track
+panel = biograpy.Panel(fig1)
+track = biograpy.tracks.BaseTrack()
+
+# Text sequence feature
+track.add_feature(biograpy.features.TextSequence(
+        'MKKVIVIGVNHAGTSFIRTLLSKSKDFQVNAYDRNTNISFLGCGIALAVSGVVKNTEDLFYSTPEELKAMGANVFMAHDVVGLDLDKKQVIVKDL',
+        start=10, name="TextSequence1"))
+
+"""
+Pretty text sequence feature allows to pass a text sequence together with a list of regions
+to highlight. The font size is calculated automatically to fit the scale of the x axis.
+"""
+
+prettyTextFeat = biograpy.features.PrettyTextSequence(
+    'KSKDFQVNAYDRNMKKVIVIGVNHAGTSFIRTLLSKSKDFQVNAYDRNTNISFLGCGIALAVSGVVKNTEDLFYSTPEELKAMGANVFMAHDVVGLDLDKKQVIVKDLATGKETVDHY',
+    highlightList=[{'start':0, 'end':10, 'background_color':'red', 'background_color_alpha':0.4, 'weight':900},
+                   {'start':20, 'end':25, 'foreground_color':'blue', 'weight':100}
+                  ],
+    start=20, name='PrettyTextSequence1')
+track.add_feature(prettyTextFeat)
+
+panel.add_track(track)
+panel.save('biograpy_test2.png')
+panel._draw_tracks()
+```
+
+![example1](/examples/biograpy_test2.png)

_config.yml

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+theme: jekyll-theme-cayman

biograpy.egg-info/PKG-INFO

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+Metadata-Version: 1.1
+Name: biograpy
+Version: 1.1.dev0
+Summary: UNKNOWN
+Home-page: UNKNOWN
+Author: Andrea Pierleoni
+Author-email: apierleoni.dev@gmail.com
+License: LGPL
+Description: BioGraPy - Biological Graphical Library in Python
+        =================================================
+
+        Fork that adds support to plot the tracks below an existing figure, and adds some new features to draw such as text sequence with automatic font size and highlighted text.
+
+        ```python
+        import matplotlib
+        import matplotlib.pyplot as plt
+        from matplotlib.font_manager import FontProperties
+        import numpy as np
+
+        import biograpy
+        from Bio.SeqFeature import SeqFeature, FeatureLocation
+        from Bio.Seq import Seq
+
+
+        fig1, ax = plt.subplots(figsize=(10,3), dpi=300)
+
+        ax.scatter(x=list(range(0, 1200)), y=np.random.random(1200))
+        ax.set_xlim([0,1200])
+        ax.set_ylim([0,2])
+
+        # We use the package biograpy to create Panel, tracks, and features
+        panel = biograpy.Panel(fig1)
+        track = biograpy.tracks.BaseTrack()
+
+        # Simple feature drawn as a rectangle
+        track.add_feature(biograpy.features.Simple(name='Simple1', start = 50, end = 300))
+
+        # Gene feature drawn as an arrow
+        genefeat = SeqFeature(FeatureLocation(100,500), type='gene', strand=1)
+        track.add_feature(biograpy.features.GeneSeqFeature(genefeat, name='GeneSeqFeature1'))
+
+        # Simple feature with color
+        track.add_feature(biograpy.features.Simple(name='Simple_colored1', start = 500, end = 820, color_by_cm=False, fc='r'))
+
+        # Gene feature with color
+        track.add_feature(biograpy.features.GeneSeqFeature(genefeat,name='GeneSeqFeature2_colored',fc='r'))
+
+        # Very short gene feature (to test the arrow head automatic sizing)
+        genefeat = SeqFeature(FeatureLocation(800,810), type='gene', strand=1)
+        track.add_feature(biograpy.features.GeneSeqFeature(genefeat, name='GeneSeqFeature_very_short'))
+
+        # mRNA with one CDS drawn as a shaded rectangle with an arrow on top
+        CDS_feature = SeqFeature(FeatureLocation(180,1000), type='CDS', strand=-1)
+        mRNA_feature = SeqFeature(FeatureLocation(180,1100), type='mRNA', strand=-1)
+        mRNAandCDSfeat = biograpy.features.CoupledmRNAandCDS(mRNA_feature, CDS_feature,
+                                                             name='CoupledmRNAandCDS1_strandm', ec='k')
+        track.add_feature(mRNAandCDSfeat)
+
+        # mRNA with CDS, custom color
+        CDS_feature = SeqFeature( FeatureLocation(200,600), type='CDS', strand=1)
+        mRNA_feature = SeqFeature( FeatureLocation(100,800), type='mRNA', strand=1)
+        mRNAandCDSfeat = biograpy.features.CoupledmRNAandCDS(mRNA_feature, CDS_feature,
+                                                             name='CoupledmRNAandCDS1_strandp_colored', ec='r', fc='r')
+        track.add_feature(mRNAandCDSfeat)
+
+        # Very short mRNA with CDS (to test the arrow head automatic sizing)
+        CDS_feature = SeqFeature( FeatureLocation(250,260), type='CDS', strand=1)
+        mRNA_feature = SeqFeature( FeatureLocation(220,300), type='mRNA', strand=1)
+        mRNAandCDSfeat = biograpy.features.CoupledmRNAandCDS(mRNA_feature, CDS_feature,
+                                                             name='CoupledmRNAandCDS1_very_short')
+        track.add_feature(mRNAandCDSfeat)
+
+        # Gene feature on minus strand
+        geneSeqfeat = SeqFeature( FeatureLocation(900,200), type = 'gene', strand=-1)
+        genefeat = biograpy.features.GeneSeqFeature(geneSeqfeat, name='GeneSeqFeature3_strandm')
+        track.add_feature(genefeat)
+
+        track2 = biograpy.tracks.BaseTrack(biograpy.features.Simple(name='Simple3_track2', start= 0, end = 80))
+
+        panel.add_track(track)
+        panel.add_track(track2)
+        panel._draw_tracks()
+        panel.save('biograpy_test1.png')
+        ```
+
+        ![example1](/examples/biograpy_test1.png)
+
+        ```python
+        fig1, ax = plt.subplots(figsize=(11,3), dpi=400)
+
+        ax.scatter(x=list(range(0, 100)), y=np.random.random(100))
+        ax.set_xlim([0,100])
+        ax.set_ylim([0,2])
+
+        # Create panel and track
+        panel = biograpy.Panel(fig1)
+        track = biograpy.tracks.BaseTrack()
+
+        # Text sequence feature
+        track.add_feature(biograpy.features.TextSequence(
+                'MKKVIVIGVNHAGTSFIRTLLSKSKDFQVNAYDRNTNISFLGCGIALAVSGVVKNTEDLFYSTPEELKAMGANVFMAHDVVGLDLDKKQVIVKDL',
+                start=10, name="TextSequence1"))
+
+        """
+        Pretty text sequence feature allows to pass a text sequence together with a list of regions
+        to highlight. The font size is calculated automatically to fit the scale of the x axis.
+        """
+
+        prettyTextFeat = biograpy.features.PrettyTextSequence(
+            'KSKDFQVNAYDRNMKKVIVIGVNHAGTSFIRTLLSKSKDFQVNAYDRNTNISFLGCGIALAVSGVVKNTEDLFYSTPEELKAMGANVFMAHDVVGLDLDKKQVIVKDLATGKETVDHY',
+            highlightList=[{'start':0, 'end':10, 'background_color':'red', 'background_color_alpha':0.4, 'weight':900},
+                           {'start':20, 'end':25, 'foreground_color':'blue', 'weight':100}
+                          ],
+            start=20, name='PrettyTextSequence1')
+        track.add_feature(prettyTextFeat)
+
+        panel.add_track(track)
+        panel.save('biograpy_test2.png')
+        panel._draw_tracks()
+        ```
+
+        ![example1](/examples/biograpy_test2.png)
+        .. _history:
+
+        Changelog
+        =========
+
+        1.1 alpha
+        ---------------------
+        - Added novel feature types: PrettyTextSequence, CoupledmRNAandCDS
+        - Added option of drawing the panel below an existing matplotlib figure
+
+        1.0 beta 
+        ---------------------
+
+        - Completed API documentation.
+        - Bug fix
+
+        1.0 alpha 
+        ---------------------
+        Major revision
+
+        - Added novel feature type: PlotFeature, BarPlotFeature
+          TextSequence
+        - Added colorbars
+        - Can now use sequence as X tick labels
+        - Improved track and figure positioning
+        - Added per-letter annotation support
+        - Added url in SVG as alternative to 
+          HTML maps
+        - Added legend for tracks
+        - Many bug fix and minor improvements
+
+        0.3 (released)
+        ---------------------
+
+        - changed namespace to biograpy
+        - Public release
+
+        0.2 (unreleased)
+        ---------------------
+
+        - boxes and imagemap [mauro]
+
+        0.1 (unreleased)
+        ---------------------
+
+        - Initial draft
+
+
+
+        .. _authors:
+
+        =======
+        AUTHORS
+        =======
+
+        * Andrea Pierleoni
+
+        ============
+        CONTRIBUTORS
+        ============
+
+        * Mauro Amico
+        * Marc Weber
+Platform: UNKNOWN
+Classifier: Programming Language :: Python

biograpy.egg-info/SOURCES.txt

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+README.md
+setup.cfg
+setup.py
+biograpy/__init__.py
+biograpy/drawer.py
+biograpy/features.py
+biograpy/seqrecord.py
+biograpy/tracks.py
+biograpy.egg-info/PKG-INFO
+biograpy.egg-info/SOURCES.txt
+biograpy.egg-info/dependency_links.txt
+biograpy.egg-info/entry_points.txt
+biograpy.egg-info/namespace_packages.txt
+biograpy.egg-info/not-zip-safe
+biograpy.egg-info/requires.txt
+biograpy.egg-info/top_level.txt

biograpy.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+