semin-egor 0.9.2 → 0.9.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (5) hide show
  1. data/History.txt +26 -37
  2. data/README.markdown +45 -35
  3. data/egor.gemspec +3 -3
  4. data/lib/egor.rb +1 -1
  5. metadata +2 -2
data/History.txt CHANGED
@@ -1,49 +1,38 @@
1
- == 0.9.0 version
1
+ == 0.9.0, released 2009-2-13
2
2
 
3
- * 5 major enhancement:
4
- * --heatmap option has been added to generate heat maps from substitution tables
5
- * --heatmap-format option has been added for heat map figure format (PNG, GIF, JPG, BMP, and PDF)
6
- * --heatmap-stem option has been added to set a file name for total heat maps figure when --heatmap 1 or 2 is set
7
- * --heatmap-columns option has been added to set the number of tables in a row when --heatmap 1 or 2 is set
8
- * --heatmap-value option has been added to print values in the cells of heat maps
3
+ * Added --heatmap option for heat map generation from substitution tables
4
+ * Added --heatmap-format option for heat map figure format (PNG, GIF, JPG, BMP, and PDF)
5
+ * Added --heatmap-stem option to set a file name of total heat maps figure when --heatmap 1 or 2 is set
6
+ * Added --heatmap-columns option to set the number of tables in a row when --heatmap 1 or 2 is set
7
+ * Added --heatmap-value option to print values in the cells of heat maps
8
+ * Renamed --noround option to --noroundoff
9
+ * 'simple_memoize' RubyGem package is no longer required
9
10
 
10
- * 2 minor enhancement:
11
- * --noround option has been renamed to --noroundoff
12
- * 'simple_memoize' RubyGem package is no longer required
11
+ == 0.0.5, released 2009-1-23
13
12
 
14
- == 0.0.5 2009-1-23
13
+ * Warns if your sigma value is too big for any amino acid count (minimum ratio of amino acid count to sigma value: 500.0)
14
+ * Added --augosigma option to avoid excessive influence of background frequencies
15
+ * Added --noround option was added to get original log odds ratios
16
+ * Added --p1smooth option was added to enable p1 probability smoothing when partial smoothing
17
+ * Fixed a bug in p2 probability calculation of the partial smoothing procedure
18
+ * Fixed a bug in total probability/log odds ratio calculation
19
+ * Changed default verbosity from ERROR to WARN
20
+ * Refactored codes to be more human readable and DRY
15
21
 
16
- * 4 major enhancement:
17
- * 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)
18
- * --augosigma option was added to avoid excessive influence of background frequencies
19
- * a bug in p2 probability calculation of the partial smoothing procedure was fixed
20
- * a bug in total probability/log odds ratio calculation was fixed
22
+ == 0.0.4, released 2008-12-15
21
23
 
22
- * 4 minor enhancement:
23
- * --noround option was added to get original log odds ratios
24
- * --p1smooth option was added to enable p1 probability smoothing when partial smoothing
25
- * default verbosity has been changed from ERROR to WARN
26
- * codes were refactored to be more human readable and DRY
27
-
28
- == 0.0.4 2008-12-15
29
-
30
- * 2 major enhancement:
31
- * log-odds ratio matrices can be generated with --nosmooth option
32
- * safe handling for zero observations or mutations of amino acids
24
+ * Fixed a bug to generated log-odds ratio matrices with --nosmooth option
25
+ * Copes with no observations or mutations
33
26
 
34
27
  == 0.0.3 2008-12-09
35
28
 
36
- * 2 major enhancement:
37
- * An option '--cys (-j) 2' added not to distinguish J from C, so 'disulphide bond' environment feature is not prerequisite
38
- * Masking works for target amino acid, too
29
+ * Added --cys (-j) 2 not to distinguish J from C, so 'disulphide bond' environment feature is not prerequisite
30
+ * Fixed a bug to make masking works for target amino acid, too
39
31
 
40
- == 0.0.2 2008-11-13
32
+ == 0.0.2, released 2008-11-13
41
33
 
42
- * 2 major enhancement:
43
- * Constrained environment features are properly handled
44
- * Sane log-odds ratio matrices are produced
34
+ * Supports user provided constrained environment features are properly handled
45
35
 
46
- == 0.0.1 2008-11-07
36
+ == 0.0.1, released 2008-11-07
47
37
 
48
- * 1 major enhancement:
49
- * Initial release
38
+ * Initial release
data/README.markdown CHANGED
@@ -165,26 +165,21 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
165
165
 
166
166
  10. Then, it will produce a file containing all the matrices, which will look like the one below. For more details, please check this [notes](http://www-cryst.bioc.cam.ac.uk/~kenji/subst/NOTES "Kenji's NOTES").
167
167
 
168
- #
169
168
  # Environment-specific amino acid substitution matrices
170
- # Creator: egor version 0.0.4
171
- # Creation Date: 20/01/2009 14:45
169
+ # Creator: egor version 0.0.5
170
+ # Creation Date: 05/02/2009 17:29
172
171
  #
173
172
  # Definitions for structural environments:
174
- # 5 features used
173
+ # 2 features used
175
174
  #
176
175
  # secondary structure and phi angle;HEPC;HEPC;F;F
177
176
  # solvent accessibility;TF;Aa;F;F
178
- # hydrogen bond to DNA;TF;Hh;F;F
179
- # water-mediated hydrogen bond to DNA;TF;Ww;F;F
180
- # van der Waals contact to DNA;TF;Vv;F;F
181
- #
182
177
  # (read in from classdef.dat)
183
178
  #
184
- # Number of alignments: 86
179
+ # Number of alignments: 1187
185
180
  # (list of .tem files read in from TEMLIST)
186
181
  #
187
- # Total number of environments: 64
182
+ # Total number of environments: 8
188
183
  #
189
184
  # There are 21 amino acids considered.
190
185
  # ACDEFGHIKLMNPQRSTVWYJ
@@ -193,34 +188,49 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
193
188
  # J: Cysteine (the free thiol form)
194
189
  #
195
190
  # Weighting scheme: clustering at PID 60 level
196
- #
197
191
  # ...
198
192
  #
199
- >HAHWV 0
193
+ >HA 0
200
194
  # A C D E F G H I K L M N P Q R S T V W Y J
201
- A 5 -6 0 0 -2 0 -2 -1 -1 -1 1 -1 -1 0 -1 1 0 0 -2 -2 -2
202
- C -7 28 -8 -49 -3 -49 -2 -1 -11 -5 -1 -49 -6 -49 -49 -4 -6 -4 -49 3 9
203
- D 0 -7 7 2 -3 0 0 -4 0 -3 -3 2 0 0 -2 1 0 -3 -5 -3 -6
204
- E 0 -68 2 5 -3 -1 -1 -3 0 -3 -1 0 0 1 -1 0 0 -3 -3 -2 -7
205
- F -2 -3 -3 -4 8 -4 -1 2 -4 1 0 -4 -4 -4 -4 -4 -2 1 2 3 -5
206
- G 0 -67 0 -1 -4 9 -3 -4 -2 -3 -4 1 -1 -2 -3 0 -2 -3 -3 -3 -2
207
- H -2 -2 0 -1 -1 -3 11 -3 -2 -3 -2 0 -2 -1 -1 -1 -1 -3 -2 0 -4
208
- I -1 -1 -4 -3 2 -4 -3 6 -3 2 2 -4 -2 -2 -4 -3 -1 3 -1 0 -4
209
- K -1 -10 0 0 -4 -2 -1 -3 5 -3 -2 0 0 1 2 -1 -1 -3 -4 -2 -5
210
- L -1 -5 -3 -3 1 -3 -3 2 -3 5 2 -4 -1 -2 -2 -3 -1 1 0 -1 -4
211
- M 1 -1 -3 -1 0 -4 -2 2 -3 2 8 -2 -2 -1 -2 -2 -1 1 -1 -1 -4
212
- N -1 -66 2 0 -4 1 0 -4 0 -4 -2 8 -1 0 -1 1 0 -3 -5 -4 -5
213
- P -1 -6 0 0 -3 -1 -2 -2 -1 -1 -2 -1 9 -1 -2 0 0 -2 -4 -3 -7
214
- Q 0 -66 0 1 -4 -2 -1 -2 1 -2 -1 0 -1 6 0 0 -1 -2 -2 -2 -6
215
- R -1 -69 -1 0 -4 -3 -1 -3 2 -2 -1 -1 -2 0 6 -1 -1 -3 -3 -2 -6
216
- S 1 -4 1 0 -3 0 -1 -3 -1 -3 -2 1 0 0 -1 5 2 -2 -3 -1 -3
217
- T 0 -5 -1 -1 -2 -2 -1 -1 -1 -1 -1 0 0 -1 -1 2 5 -1 -3 -2 -3
218
- V 0 -4 -3 -3 1 -4 -3 3 -3 1 1 -3 -2 -2 -3 -2 -1 6 0 -1 -2
219
- W -2 -61 -5 -3 2 -3 -2 -1 -4 0 -1 -5 -4 -2 -3 -3 -3 0 14 3 -6
220
- Y -2 3 -3 -2 4 -3 0 0 -2 0 0 -4 -3 -2 -2 -1 -2 0 3 9 -3
221
- J -3 9 -7 -8 -5 -2 -4 -4 -6 -4 -4 -5 -7 -6 -6 -3 -3 -2 -6 -3 15
222
- U -3 15 -7 -8 -5 -3 -4 -4 -6 -4 -4 -5 -7 -6 -6 -3 -3 -2 -6 -3 15
223
- ...
195
+ A 3 -5 0 0 -1 2 0 0 1 0 0 0 1 1 0 1 1 1 -1 0 2
196
+ C -16 19 -16 -18 -11 -14 -13 -13 -14 -14 -14 -11 -17 -16 -13 -16 -14 -12 -12 -10 -4
197
+ D 1 -7 6 3 -3 1 0 -3 1 -3 -2 2 1 2 0 1 0 -2 -3 -2 -2
198
+ E 3 -7 5 7 -1 2 2 0 3 0 0 3 2 4 3 3 2 1 -1 0 -1
199
+ F -4 -4 -6 -6 7 -5 -1 0 -4 1 0 -5 -5 -4 -4 -4 -3 -1 3 3 0
200
+ G -2 -6 -3 -4 -5 5 -4 -5 -4 -5 -4 -2 -3 -4 -4 -2 -3 -5 -6 -4 -3
201
+ H 0 -6 0 0 1 0 8 -1 0 0 0 1 -2 1 1 0 0 0 1 3 0
202
+ I -3 -7 -6 -5 0 -5 -3 4 -4 1 1 -5 -4 -4 -3 -5 -2 2 -2 -1 0
203
+ K 2 -6 2 2 -1 1 2 0 5 1 1 2 0 3 4 2 2 0 -2 0 -1
204
+ L -2 -6 -5 -4 1 -4 -2 2 -3 4 2 -3 -4 -3 -2 -4 -2 1 0 0 1
205
+ M -2 -7 -4 -3 1 -2 -1 2 -2 2 6 -3 -4 -2 -1 -2 -1 1 0 0 1
206
+ N 0 -5 1 0 -3 1 1 -3 0 -2 -2 6 -2 0 0 1 1 -2 -3 -1 -1
207
+ P -1 -7 -1 -2 -4 -1 -3 -3 -2 -3 -4 -2 9 -2 -3 0 -1 -2 -4 -4 -4
208
+ Q 2 -7 2 2 -1 1 2 -1 2 0 0 2 0 5 2 1 1 0 -2 -1 0
209
+ R 1 -6 1 1 -1 0 2 0 3 0 1 1 -1 2 6 1 1 0 -1 0 0
210
+ S 0 -6 -1 -1 -3 0 -2 -3 -1 -3 -3 0 0 -1 -1 3 1 -2 -4 -3 0
211
+ T -1 -7 -2 -2 -3 -2 -2 -2 -2 -2 -2 -1 -2 -2 -2 0 3 -1 -3 -3 0
212
+ V -3 -6 -6 -5 -1 -4 -3 1 -4 0 0 -5 -3 -4 -4 -4 -2 2 -2 -2 0
213
+ W -4 -6 -6 -5 2 -6 -2 -2 -5 -1 -2 -5 -5 -4 -4 -5 -4 -2 12 2 -3
214
+ Y -3 -5 -5 -5 3 -4 1 -1 -3 -1 -1 -3 -5 -3 -3 -4 -3 -2 3 7 -1
215
+ J -2 0 -4 -5 0 -2 -1 0 -3 0 0 -3 -6 -2 -2 -1 -1 0 -1 0 9
216
+ U -5 16 -7 -8 -3 -5 -4 -3 -6 -3 -3 -5 -9 -6 -5 -4 -4 -3 -4 -3 6
217
+ ...
218
+
219
+ 11. To generate a heat map for each table with values in it,
220
+
221
+ ~user $ egor -l TEMLIST --heatmap 0 --heatmap-value
222
+
223
+ which will look like this,
224
+
225
+ <img alt="Sample Heat Map" style="border-width:0" src="http://www-cryst.bioc.cam.ac.uk/~semin/images/0. HA.png">
226
+
227
+ 12. To generate one big figure, 'myheatmaps.gif' containing all the heat maps (4 maps in a row),
228
+
229
+ ~user $ egor -l TEMLIST --heatmap 1 --heatmap-stem myheatmaps --heatmap-format 1 --heatmap-columns 4
230
+
231
+ which will look like this,
232
+
233
+ <img alt="Sample Heat Maps" style="border-width:0" src="http://www-cryst.bioc.cam.ac.uk/~semin/images/myheatmaps.gif">
224
234
 
225
235
  ## Repository
226
236
 
data/egor.gemspec CHANGED
@@ -2,11 +2,11 @@
2
2
 
3
3
  Gem::Specification.new do |s|
4
4
  s.name = %q{egor}
5
- s.version = "0.9.2"
5
+ s.version = "0.9.3"
6
6
 
7
7
  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
8
8
  s.authors = ["Semin Lee"]
9
- s.date = %q{2009-02-12}
9
+ s.date = %q{2009-02-13}
10
10
  s.default_executable = %q{egor}
11
11
  s.email = ["seminlee@gmail.com"]
12
12
  s.executables = ["egor"]
@@ -18,7 +18,7 @@ Gem::Specification.new do |s|
18
18
  s.require_paths = ["lib"]
19
19
  s.rubyforge_project = %q{egor}
20
20
  s.rubygems_version = %q{1.3.1}
21
- s.summary = "A new ESST generator"
21
+ s.summary = 'A new ESST generator'
22
22
  s.test_files = ["test/test_string_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_egor_cli.rb", "test/test_egor_environment_class_hash.rb", "test/test_math_extensions.rb", "test/test_helper.rb", "test/test_egor_environment_feature.rb", "test/test_narray_extensions.rb", "test/test_egor.rb"]
23
23
 
24
24
  if s.respond_to? :specification_version then
data/lib/egor.rb CHANGED
@@ -2,5 +2,5 @@ $:.unshift(File.dirname(__FILE__)) unless
2
2
  $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
3
3
 
4
4
  module Egor
5
- VERSION = '0.9.2'
5
+ VERSION = '0.9.3'
6
6
  end
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: semin-egor
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.9.2
4
+ version: 0.9.3
5
5
  platform: ruby
6
6
  authors:
7
7
  - Semin Lee
@@ -9,7 +9,7 @@ autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
11
 
12
- date: 2009-02-12 00:00:00 -08:00
12
+ date: 2009-02-13 00:00:00 -08:00
13
13
  default_executable: egor
14
14
  dependencies:
15
15
  - !ruby/object:Gem::Dependency