new files

Author: jheled@gmail.com

doc/tree2.png

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+==============
+Tree Utilities
+==============
+
+------------------
+root_unrooted_tree
+------------------
+
+    Heuristically root an unrooted (or rooted) tree using either
+    midpoint rooting or the root position which minimizes the variance
+    of tip ages.
+
+Usage:
+^^^^^^
+
+::
+
+  Root using midpoint rooting.
+  
+| **$ root_unrooted_tree  -m '(a:1,b:2,c:3)'**
+| ((a:1,b:2):0.5,c:2.5)
+
+::
+
+  Root using minimim variance.
+  
+| **$ root_unrooted_tree  '(a:1,b:2,c:3)'**
+| ((a:1,b:2):0.75,c:2.25)
+
+
+---------
+tree2tikz
+---------
+
+    Generate `tikz code <http://en.wikipedia.org/wiki/PGF/TikZ/>`_ for
+    a NEWICK tree. At the moment quite primitive, and the single
+    example below shows the full capabilites. However, it may prove
+    easier than starting from scratch.
+    
+Usage:
+^^^^^^
+
+::
+
+  Generate a tree with some (red) marked nodes, and a vertical line passes through them and the root.
+  
+| **$ tree2tikz --standalone --style 'marked=thick,red,fill' -o auto '(((A:1,B:1):1,C:2)[&style=marked,vline=hline]:5,(((D:1.5,E:1.5):2.5,((F:1,G:1):1.5,H:2.5):1.5)[&style=marked,vline=hline]:2,(I:2.75,K:2.75):3.5):0.75)[&vline=hline]'**
+
+.. image:: tree2.png
+
+

doc/trees.rst

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+from __future__ import division
+from math import log,exp
+
+from calign import globalAlign, createProfile, profileAlign, distances, DIVERGENCE, IDENTITY, JCcorrection
+
+#scores = (10,-5,-6,None,False)
+scores = (10,-5,-6,-6,False)
+fescores = (10,-5,-6,-6,True)
+
+s1 = """AAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTAGTGATTGCCATCTTGGCTTAAACTATATCCATCTACACCTGTGAACTGTTTGATTGAATCTCACGATTCAATTCTTTACAAACATTGTGTAATGAACGTCATTAGATCATAACAAAAAAACTTTAACTAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGGTCATAGCTGTTTCC"""
+
+s2 = """AAGTCGTAACGAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTAAAGGTTTCGGGTACCCAGTGCCCAAACTTCAACCCTATGTTTTAACTATACATGTTTCTTTGCCGGTTTCGGCCGGCAGAAGTTTTCTCAAACTCATTATAAATGTGTCTTCTGAATCAAAACTAAATAAATTATAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGGTCATAGCTGTTTCCTG"""
+
+s3 = """CGCAGTGGGGTGGTGTGCTCGATGTGGCCGGTGCCGATCGCGTGACCGTTGGCCGTCAACGTCACGGTGCCGCCTTTGCCGAAATCCTTAGGGCCGCCGTCGTATTTGAAGTTGAATCCCAGTGTGACCCTGCCGGTCGGAACTGACTGGCTCGACGTCACCCGGTAGCGCGCGGCATCGATGAAGAACGCAGCGGTCATAGCTGTTTCCTG"""
+
+def test00() :
+  """
+>>> globalAlign("AAA", "AAA", report = IDENTITY)
+1.0
+>>> globalAlign("AAA", "AAA", report = DIVERGENCE)
+0.0
+>>> 3*globalAlign("AAA", "AAC", report = IDENTITY, scores=scores)
+2.0
+>>> (globalAlign("AAA", "AAC", report = JCcorrection, scores=scores) - (-3/4. * log(5/9.))) < 1e-12
+True
+>>> globalAlign("AAGG", "AAT", report = IDENTITY, scores=scores)
+0.5
+>>> 3*globalAlign("AAGG", "AAT", report = IDENTITY, scores=fescores)
+2.0
+>>> globalAlign("AAGG", "TAA", scores=fescores)
+((5, 0, 0, 1, 1), (3, 0, 0, 5, 5))
+>>> 265.0*globalAlign(s1, s2, scores=scores, report=IDENTITY)
+188.0
+>>> 263*globalAlign(s1, s2, scores=fescores, report=IDENTITY)
+188.0
+>>> a = globalAlign(s1, s2, scores=scores) ; p = createProfile(a) ; b = profileAlign(s3,p) ; distances((b,) + a, align=0)
+(0.508, 0.4921875, 0.28517110266159695)
+"""
+  pass
+
+if __name__ == '__main__':
+  import doctest
+  doctest.testmod()
+