egor 0.0.4 → 0.0.5
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- data/History.txt +14 -0
- data/Manifest.txt +2 -0
- data/README.rdoc +2 -2
- data/lib/egor/cli.rb +553 -401
- data/lib/egor.rb +1 -1
- data/lib/environment.rb +2 -2
- data/lib/environment_class_hash.rb +18 -0
- data/lib/environment_feature_array.rb +10 -0
- data/website/index.html +2 -2
- metadata +6 -25
- data.tar.gz.sig +0 -0
- metadata.gz.sig +0 -0
data/History.txt
CHANGED
@@ -1,3 +1,17 @@
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== 0.0.5 2009-1-23
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3
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* 4 major enhancement:
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4
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* Egor warns if your sigma value is too big for any amino acid count (minimum ratio of amino acid count to sigma value: 500.0)
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5
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* --augosigma option was added to avoid excessive influence of backgournd frequencies
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* a bug in p2 probabilty calculation of the partial smoothing procedure was fixed
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* a bug in total probability/log odds ratio calculation was fixed
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* 4 minor enhancement:
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* --noround option was added to get original log odds ratios
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* --p1smooth option was added to enable p1 probability smoothing when partial smoothing
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* default verbosity has been changed from ERROR to WARN
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* codes were refactored to be more human readable and DRY
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== 0.0.4 2008-12-15
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* 2 major enhancement:
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data/Manifest.txt
CHANGED
@@ -11,7 +11,9 @@ lib/egor.rb
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lib/egor/cli.rb
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lib/enumerable_extensions.rb
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13
13
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lib/environment.rb
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14
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lib/environment_class_hash.rb
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15
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lib/environment_feature.rb
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lib/environment_feature_array.rb
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lib/math_extensions.rb
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lib/narray_extensions.rb
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lib/nmatrix_extensions.rb
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data/README.rdoc
CHANGED
@@ -34,8 +34,8 @@ egor: Esst GeneratOR, a program for calculating environment-specific substitutio
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--tem-list (-l) FILE: a list for tem files
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--classdef (-c) FILE: a file for the defintion of environments (default: 'classdef.dat')
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--outfile (-o) FILE: output filename (default 'allmat.dat')
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-
--weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting
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-
--noweight: calculate substitution counts with no weights
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--weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting (default: 60)
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--noweight: calculate substitution counts with no weights
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--smooth (-s) INTEGER:
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0 for parial smoothing (default)
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1 for full smoothing
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