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

[Yanbo Ye]

Thanks, Peter. I noticed the Travis CI build failed because of the
'StringIO' import error under version 3.3. Need to fix this version issue.


On Fri, Dec 13, 2013 at 12:30 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> 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
>



-- 

*Yanbo Ye*
*Guangzhou Institutes of Biomedicine and Health, *
*Chinese Academy of Sciences*
*190 Kaiyuan Avenue, Science Park, Guangzhou, China*

*Email: ye_yanbo at gibh.ac.cn <ye_yanbo at gibh.ac.cn>*
*Web: http://www.yeyanbo.com <http://www.yeyanbo.com>*
*Phone: (86)-020-32093810*