[Biopython-dev] Fwd: [biopython] TreeConstruction and Consensus modules from GSoC 2013 (#270)

[Peter Cock]

Hello Biopythoneers,

For those of you not following the GitHub repository,
this is quite a big and important pull request :)

Please take a look!

Thanks,

Peter

---------- Forwarded message ----------
From: yeyanbo <notifications at github.com>
Date: Thu, Dec 12, 2013 at 2:16 PM
Subject: [biopython] TreeConstruction and Consensus modules from GSoC
2013 (#270)
To: biopython/biopython <biopython at noreply.github.com>


two module files created in Bio/Phylo: TreeConstruction.py, Consensus.py ;
two test files created in Tests: test_TreeConstruction.py , test_Consensus.py ;
directory created for testing files: Tests\TreeConstruction .

________________________________

You can merge this Pull Request by running

  git pull https://github.com/lijax/biopython master

Or view, comment on, or merge it at:

  https://github.com/biopython/biopython/pull/270

Commit Summary

add TreeConststruction and Consensus modules
implement upgma and nj algorithms"
add parsimony scorer
rewrite and test parsimony score
minor change
add NNITreeSearcher._get_neighbors
complete parsimony method
fix the bug that the nj tree may have 1 child instead of 3 at the root
add convertion from SubsMat to Matrix for protein submatrix
BitString and strict_consensus
reorganize different tests
add automatic test for consensus tree
add `repr` funcionn for Matrix class and improve the document
move `delitem` and `insert` from DistanceMatrix to Matrix
fix the index bug of Matrix.insert() function and improve the document
test files for consensus algorithms
improve document of DiscanceCalculator and DistanceTreeConstructor
improve document for parsimony tree classes
majority and adam consensus methods
fix majority bug, finish adam consensus, doc improvement
add branch support method
change DistanceCalculator parameters as msa should be independent
restructure TreeConstructor classes
fix nj bug
assign 0 lenght to root clade of nj and upgma
add bootstrap method
adapt "identity" model in DistanceCalculator to protein;None condition
of starting_tree in ParsimonyTreeConstructor
convert list to generator in bootstrap methods
fix adam consensus bug
test cleanup
minor change
make assistant classes private
remove import *

File Changes

A Bio/Phylo/Consensus.py (570)
A Bio/Phylo/TreeConstruction.py (1011)
A Tests/TreeConstruction/adam_refs.tre (3)
A Tests/TreeConstruction/bootstrap_consensus.tre (1)
A Tests/TreeConstruction/consensus_refs.tre (3)
A Tests/TreeConstruction/majority_ref.tre (2)
A Tests/TreeConstruction/msa.phy (6)
A Tests/TreeConstruction/neighbor_trees.tre (4)
A Tests/TreeConstruction/nj.tre (1)
A Tests/TreeConstruction/pars1.tre (1)
A Tests/TreeConstruction/pars2.tre (1)
A Tests/TreeConstruction/pars3.tre (1)
A Tests/TreeConstruction/strict_refs.tre (3)
A Tests/TreeConstruction/test.log (36)
A Tests/TreeConstruction/trees.tre (3)
A Tests/TreeConstruction/upgma.tre (1)
A Tests/test_Consensus.py (152)
A Tests/test_TreeConstruction.py (245)

Patch Links:

https://github.com/biopython/biopython/pull/270.patch
https://github.com/biopython/biopython/pull/270.diff