Merge 74dd6ac into 7ae7464

rigdenlab · Mar 14, 2018 · b7ca3cf · b7ca3cf
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -2,6 +2,25 @@
 Changelog
 =========
 
+[Unreleased]
+------------
+Added
+~~~~~
+- ``conkit.plot`` subpackage refactored to allow ``matplotlib`` access of ``Figure`` instances. This provides
+  functionality similar to ``seaborn``, so ``matplotlib.Axes`` can be provided into which a plot is drawn.
+- ``ContactMap.as_list`` function to represent the contact map as a 2D-list of residue indexes
+- ``conkit.misc.normalize`` function to apply Feature scaling normalization
+- ``CONTRIB.rst`` file to list all contributors
+- ``SequenceFile.diversity`` property defined by :math:`\sqrt{N}/L`
+- ``ContactMap.reindex`` to reindex a contact map given a new starting index
+- ``ContactMap.singletons`` returns a copy of the contact map with singleton contacts, i.e. ones without neighbors
+Changed
+~~~~~~~
+- Changed API interface for ``conkit.plot`` in accordance to necessary changes for above
+- ``ContactMapFigure`` now accepts ``lim`` parameters for axes limits
+- ``ContactMapFigure`` and ``ContacctMapChordFigure`` improved to better space marker size
+- Typos corrected in documentation 
+
 [0.8.4]
 -------
 Added

diff --git a/CONTRIB.rst b/CONTRIB.rst
@@ -0,0 +1,10 @@
+
+Contributors
+============
+
+This is a list of people who have made contributions to ConKit.
+
+- `Daniel Rigden <https://github.com/DanielRigden>`_
+- `Felix Simkovic <https://github.com/fsimkovic>`_
+- `Jens Thomas <https://github.com/DanielRigden>`_
+- `Stefan Seemayer <https://github.com/sseemayer>`_
diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2016, University of Liverpool
+Copyright (c) 2016-18, University of Liverpool
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

diff --git a/README.rst b/README.rst
@@ -62,17 +62,4 @@ Found a Bug?
 ++++++++++++
 Please use the `GitHub Issue Tracker`_.
 
-Contributors
-++++++++++++
-
-- `Felix Simkovic <https://github.com/fsimkovic>`_
-- `Jens Thomas <https://github.com/linucks>`_
-- `Daniel Rigden <https://github.com/DanielRigden>`_
-
-
-Ackowledgements
-+++++++++++++++
-- `Stefan Seemayer <https://github.com/sseemayer>`_
-
-
 .. _GitHub Issue Tracker: https://github.com/rigdenlab/conkit/issues
diff --git a/conkit/__init__.py b/conkit/__init__.py
@@ -1,6 +1,6 @@
 # BSD 3-Clause License
 #
-# Copyright (c) 2016-17, University of Liverpool
+# Copyright (c) 2016-18, University of Liverpool
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without

diff --git a/conkit/applications/__init__.py b/conkit/applications/__init__.py
@@ -2,7 +2,7 @@
 #
 # BSD 3-Clause License
 #
-# Copyright (c) 2016-17, University of Liverpool
+# Copyright (c) 2016-18, University of Liverpool
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without

diff --git a/conkit/applications/bbcontacts.py b/conkit/applications/bbcontacts.py
@@ -2,7 +2,7 @@
 #
 # BSD 3-Clause License
 #
-# Copyright (c) 2016-17, University of Liverpool
+# Copyright (c) 2016-18, University of Liverpool
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without

diff --git a/conkit/applications/ccmpred.py b/conkit/applications/ccmpred.py
@@ -2,7 +2,7 @@
 #
 # BSD 3-Clause License
 #
-# Copyright (c) 2016-17, University of Liverpool
+# Copyright (c) 2016-18, University of Liverpool
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without

diff --git a/conkit/applications/cdhit.py b/conkit/applications/cdhit.py
@@ -2,7 +2,7 @@
 #
 # BSD 3-Clause License
 #
-# Copyright (c) 2016-17, University of Liverpool
+# Copyright (c) 2016-18, University of Liverpool
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without

diff --git a/conkit/applications/hhblits.py b/conkit/applications/hhblits.py
@@ -2,7 +2,7 @@
 #
 # BSD 3-Clause License
 #
-# Copyright (c) 2016-17, University of Liverpool
+# Copyright (c) 2016-18, University of Liverpool
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without

diff --git a/conkit/applications/hhfilter.py b/conkit/applications/hhfilter.py
@@ -2,7 +2,7 @@
 #
 # BSD 3-Clause License
 #
-# Copyright (c) 2016-17, University of Liverpool
+# Copyright (c) 2016-18, University of Liverpool
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without

diff --git a/conkit/applications/jackhmmer.py b/conkit/applications/jackhmmer.py
@@ -2,7 +2,7 @@
 #
 # BSD 3-Clause License
 #
-# Copyright (c) 2016-17, University of Liverpool
+# Copyright (c) 2016-18, University of Liverpool
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without

diff --git a/conkit/applications/psicov.py b/conkit/applications/psicov.py
@@ -2,7 +2,7 @@
 #
 # BSD 3-Clause License
 #
-# Copyright (c) 2016-17, University of Liverpool
+# Copyright (c) 2016-18, University of Liverpool
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without

diff --git a/conkit/command_line/__init__.py b/conkit/command_line/__init__.py
@@ -1,6 +1,6 @@
 # BSD 3-Clause License
 #
-# Copyright (c) 2016-17, University of Liverpool
+# Copyright (c) 2016-18, University of Liverpool
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without

diff --git a/conkit/command_line/conkit_convert.py b/conkit/command_line/conkit_convert.py
@@ -2,7 +2,7 @@
 #
 # BSD 3-Clause License
 #
-# Copyright (c) 2016-17, University of Liverpool
+# Copyright (c) 2016-18, University of Liverpool
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without

diff --git a/conkit/command_line/conkit_msatool.py b/conkit/command_line/conkit_msatool.py
@@ -2,7 +2,7 @@
 #
 # BSD 3-Clause License
 #
-# Copyright (c) 2016-17, University of Liverpool
+# Copyright (c) 2016-18, University of Liverpool
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without
@@ -46,30 +46,30 @@
 import conkit.command_line
 import conkit.io
 import conkit.plot
+import conkit.plot.tools
 
 logger = None
 
 
 def main():
-    parser = argparse.ArgumentParser(
-        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
     parser.add_argument('msafile', help='Multiple Sequence Alignment file')
     parser.add_argument('msaformat', help='Multiple Sequence Alignment format')
     args = parser.parse_args()
 
-    # Setup the logger
     global logger
     logger = conkit.command_line.setup_logging(level='info')
 
-    # Compute all the data
     msa = conkit.io.read(args.msafile, args.msaformat)
+
     plot = args.msafile.rsplit('.', 1)[0] + '.png'
-    conkit.plot.SequenceCoverageFigure(msa, file_name=plot)
+    figure = conkit.plot.SequenceCoverageFigure(msa, legend=True)
+    figure.ax.set_aspect(conkit.plot.tools.get_adjusted_aspect(figure.ax, 0.3))
+    figure.savefig(plot)
 
     logger.info('Input MSA File:                            %s', args.msafile)
     logger.info('Input MSA Format:                          %s', args.msaformat)
-    logger.info('Length of the Target Sequence:             %d',
-                msa.top_sequence.seq_len)
+    logger.info('Length of the Target Sequence:             %d', msa.top_sequence.seq_len)
     logger.info('Total Number of Sequences:                 %d', msa.nseq)
     logger.info('Number of Effective Sequences:             %d', msa.neff)
     logger.info('Sequence Coverage Plot:                    %s', plot)