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Pca #102

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Pca #102

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necrolyte2
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I'm not even sure what this branch was about, but putting up so we can review and what not

Panciera and others added 21 commits July 22, 2015 17:52
degen.py working with minimal tests
4a656d5
Merge branch 'master' of https://github.com/VDBWRAIR/bio_pieces
ea2eba6
@necrolyte2
Building up pca analysis for fasta sequence alignment
b253729
@necrolyte2
This notebook will build what we think is a correct 3d axis for pca a…
e61449e 
…nalysis. Will convert to regular python
@necrolyte2
Converted ipython notebook to script that takes in fasta file path an…
03942de 
…d optionally output file location
@necrolyte2
docs and allowed matrix to lookup 'all' key for values that are not i…
e83d9e3 
…n matrix
@necrolyte2
Added matplotlib to requirements. Tests now build documentation image…
15190a8 
…s. Can supply substitution matrix on command line. Fixed bug with unindexed dataframe which was very slow
@necrolyte2
Removed x,y and z tick labels. Addex X,Y Z axis labels. Added mean le…
a9db6fa 
…gend key
@necrolyte2
ipython notebook for messing around with
0b81095
@necrolyte2
adding nologcapture. Removing specific emails for build notifications…
9eb6fd0 
… as I was not getting them. By default they go to the commit author
@necrolyte2
py26 ordereddict import check
159ec02
@necrolyte2
Trying to fix matplotlib tkagg issue
21b1a2a
@necrolyte2
StringIO,BytesIO compatibility fixed for py26/27 py3
d5b0e74
Merge branch 'pca' of https://github.com/VDBWRAIR/bio_pieces into pca
22300f1
initial commit of make_pca
963beb2
added make_pca requirements: emperor,skbio
02c28de
fixed syntax bug in make_pca, added shorter test file for faster runtime
5117d65
aliased python make_pca.py as make_pca in setup.py
51f9020
added make_pca robot test
ab4c39b
fixed scikit-bio package name
60e124f
added blas to .travis.yml
a5da170
@averagehat
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The alternative lives here: #43
docs: https://github.com/averagehat/bio_pieces/blob/881256455a581886027781557b0e0601eb93d631/docs/scripts/make_pcoa.rst

I never re-opened that PR against master.

@necrolyte2
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It seems that the other PR is better as it utilizes emperor which if I remember correctly was just better overall?

@averagehat
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that's what we decided at the time. I'll re-open that PR. I wouldn't want to lose this code altogether, though, as it might be useful later, even if just as a reference. Maybe just not delete the branch?

@necrolyte2
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I don't like 'dirty' branches haha, but ya. I would just leave this PR open then with these comments otherwise might forget later why that branch exists

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@necrolyte2 @averagehat