egor 0.0.5 → 0.9.0
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- data/History.txt +28 -26
- data/Manifest.txt +12 -8
- data/README.rdoc +206 -54
- data/Rakefile +9 -9
- data/egor.gemspec +13 -15
- data/lib/egor.rb +1 -1
- data/lib/egor/cli.rb +535 -168
- data/lib/egor/environment.rb +34 -0
- data/lib/egor/environment_class_hash.rb +20 -0
- data/lib/egor/environment_feature.rb +26 -0
- data/lib/egor/environment_feature_array.rb +12 -0
- data/lib/egor/heatmap_array.rb +111 -0
- data/lib/narray_extensions.rb +3 -2
- data/lib/nmatrix_extensions.rb +227 -6
- data/lib/string_extensions.rb +17 -0
- data/test/egor/test_cli.rb +9 -0
- data/test/egor/test_environment_class_hash.rb +25 -0
- data/test/egor/test_environment_feature.rb +29 -0
- data/test/test_math_extensions.rb +11 -0
- data/test/test_narray_extensions.rb +14 -0
- data/test/test_string_extensions.rb +11 -0
- data/website/index.html +5 -76
- data/website/index.txt +183 -18
- data/website/stylesheets/screen.css +0 -1
- metadata +27 -20
- data/lib/enumerable_extensions.rb +0 -11
- data/lib/environment.rb +0 -58
- data/lib/environment_class_hash.rb +0 -18
- data/lib/environment_feature.rb +0 -14
- data/lib/environment_feature_array.rb +0 -10
- data/test/test_egor_cli.rb +0 -8
- data/test/test_enumerable_extensions.rb +0 -16
- data/test/test_environment_feature.rb +0 -11
data/History.txt
CHANGED
@@ -1,36 +1,38 @@
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1
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-
== 0.0
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1
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+
== 0.9.0 13/2/2009
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2
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3
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-
*
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4
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-
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5
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-
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6
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-
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7
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-
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3
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+
* Added --heatmap option for heat map generation from substitution tables
|
4
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+
* Added --heatmap-format option for heat map figure format (PNG, GIF, JPG, BMP, and PDF)
|
5
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+
* Added --heatmap-stem option to set a file name of total heat maps figure when --heatmap 1 or 2 is set
|
6
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+
* Added --heatmap-columns option to set the number of tables in a row when --heatmap 1 or 2 is set
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7
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+
* Added --heatmap-values option to print values in the cells of heat maps
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8
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+
* Renamed --noround option to --noroundoff
|
9
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* 'simple_memoize' RubyGem package is no longer required
|
8
10
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9
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-
|
10
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-
* --noround option was added to get original log odds ratios
|
11
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-
* --p1smooth option was added to enable p1 probability smoothing when partial smoothing
|
12
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-
* default verbosity has been changed from ERROR to WARN
|
13
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-
* codes were refactored to be more human readable and DRY
|
11
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+
== 0.0.5 23/1/2009
|
14
12
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15
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-
|
13
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+
* 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
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+
* Added --augosigma option to avoid excessive influence of background frequencies
|
15
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+
* Added --noround option was added to get original log odds ratios
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16
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+
* Added --p1smooth option was added to enable p1 probability smoothing when partial smoothing
|
17
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+
* Fixed a bug in p2 probability calculation of the partial smoothing procedure
|
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+
* Fixed a bug in total probability/log odds ratio calculation
|
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* Changed default verbosity from ERROR to WARN
|
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* Refactored codes to be more human readable and DRY
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21
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17
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-
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18
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-
* log-odds ratio matrices can be generated with --nosmooth option
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-
* safe handling for zero observations or mutations of amino acids
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== 0.0.4 15/12/2008
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21
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-
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* Fixed a bug to generated log-odds ratio matrices with --nosmooth option
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* Copes with no observations or mutations
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26
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-
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24
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-
* An option '--cys (-j) 2' added not to distinguish J from C, so 'disulphide bond' environment feature is not prerequisite
|
25
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-
* Masking works for target amino acid, too
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27
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+
== 0.0.3 09/12/2008
|
26
28
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-
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29
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* Added --cys (-j) 2 not to distinguish J from C, so 'disulphide bond' environment feature is not prerequisite
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* Fixed a bug to make masking works for target amino acid, too
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31
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-
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* Constrained environment features are properly handled
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* Sane log-odds ratio matrices are produced
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== 0.0.2 13/11/2008
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-
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* Supports user provided constrained environment features are properly handled
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-
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== 0.0.1 07/11/2008
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* Initial release
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data/Manifest.txt
CHANGED
@@ -9,24 +9,28 @@ config/website.yml.sample
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9
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egor.gemspec
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10
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lib/egor.rb
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11
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lib/egor/cli.rb
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-
lib/
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lib/
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lib/
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-
lib/
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lib/
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12
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lib/egor/environment.rb
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lib/egor/environment_class_hash.rb
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14
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lib/egor/environment_feature.rb
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15
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lib/egor/environment_feature_array.rb
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lib/egor/heatmap_array.rb
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17
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lib/math_extensions.rb
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18
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lib/narray_extensions.rb
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19
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lib/nmatrix_extensions.rb
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lib/string_extensions.rb
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21
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script/console
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script/destroy
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script/generate
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script/txt2html
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test/egor/test_cli.rb
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test/egor/test_environment_class_hash.rb
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test/egor/test_environment_feature.rb
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28
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test/test_egor.rb
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test/test_egor_cli.rb
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test/test_enumerable_extensions.rb
|
27
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-
test/test_environment_feature.rb
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29
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test/test_helper.rb
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test/test_math_extensions.rb
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31
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test/test_narray_extensions.rb
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29
32
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test/test_nmatrix_extensions.rb
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33
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test/test_string_extensions.rb
|
30
34
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website/index.html
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35
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website/index.txt
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website/javascripts/rounded_corners_lite.inc.js
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data/README.rdoc
CHANGED
@@ -1,102 +1,254 @@
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1
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= egor
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2
2
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-
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3
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http://www-cryst.bioc.cam.ac.uk/egor
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5
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==
|
6
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== Description
|
7
7
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8
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egor
|
8
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'egor' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.
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9
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10
10
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==
|
11
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== Features
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12
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*
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14
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*
|
15
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-
*
|
16
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*
|
17
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* In theory, infinite number of environment features can be handled
|
13
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+
* Environment-specific substitution table generation based on user providing environmental class definition
|
14
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* Entropy-based smoothing procedures to cope with sparse data problem
|
15
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* BLOSUM-like weighting procedures using PID threshold
|
16
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* Heat Map generation for substitution tables
|
18
17
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18
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20
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==
|
19
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== Requirements
|
21
20
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|
22
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-
|
21
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* ruby 1.8.7 or above (http://www.ruby-lang.org)
|
22
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* rubygems 1.2.0 or above (http://rubyforge.org/projects/rubygems)
|
23
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+
|
24
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Following RubyGems will be automatically installed if you have rubygems installed on your machine
|
25
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+
|
26
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+
* narray (http://narray.rubyforge.org)
|
27
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* facets (http://facets.rubyforge.org)
|
28
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* bio (http://bioruby.open-bio.org)
|
29
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* RMagick (http://rmagick.rubyforge.org)
|
30
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+
|
31
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|
32
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== Installation
|
33
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|
34
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~user $ sudo gem install egor
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23
35
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|
24
36
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|
25
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-
==
|
37
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+
== Basic Usage
|
26
38
|
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27
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-
|
28
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-
or
|
29
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-
$ egor -f TEM-file -c classdef.dat
|
39
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+
It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~kenji/subst/), so in most cases, you can swap 'subst' with 'egor'.
|
30
40
|
|
41
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+
~user $ egor -l TEMLIST-file -c classdef.dat
|
42
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+
or
|
43
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~user $ egor -f TEM-file -c classdef.dat
|
31
44
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|
32
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-
|
45
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+
|
46
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+
== Options
|
33
47
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--tem-file (-f) FILE: a tem file
|
34
48
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--tem-list (-l) FILE: a list for tem files
|
35
49
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--classdef (-c) FILE: a file for the defintion of environments (default: 'classdef.dat')
|
36
50
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--outfile (-o) FILE: output filename (default 'allmat.dat')
|
37
51
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--weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting (default: 60)
|
38
|
-
--noweight: calculate substitution
|
52
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+
--noweight: calculate substitution count with no weights
|
39
53
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--smooth (-s) INTEGER:
|
40
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-
0 for
|
54
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+
0 for partial smoothing (default)
|
41
55
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1 for full smoothing
|
56
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+
--p1smooth: perform smoothing for p1 probability calculation when partial smoothing
|
42
57
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--nosmooth: perform no smoothing operation
|
43
58
|
--cys (-y) INTEGER:
|
44
59
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0 for using C and J only for structure (default)
|
45
60
|
1 for both structure and sequence
|
46
|
-
2 for using only C for both
|
61
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+
2 for using only C for both (must be set when you have no 'disulphide' or 'disulfide' annotation in templates)
|
47
62
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--output INTEGER:
|
48
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-
0 for raw
|
63
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+
0 for raw count (no smoothing performed)
|
49
64
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1 for probabilities
|
50
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-
2 for log
|
51
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-
--
|
52
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-
--
|
53
|
-
--
|
54
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-
--
|
65
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+
2 for log odds ratios (default)
|
66
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+
--noroundoff: do not round off log odds ratio
|
67
|
+
--scale INTEGER: log odds ratio matrices in 1/n bit units (default 3)
|
68
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+
--sigma DOUBLE: change the sigma value for smoothing (default 5.0)
|
69
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+
--autosigma: automatically adjust the sigma value for smoothing
|
70
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+
--add DOUBLE: add this value to raw count when deriving log odds ratios without smoothing (default 1/#classes)
|
55
71
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--pidmin DOUBLE: count substitutions only for pairs with PID equal to or greater than this value (default none)
|
56
72
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--pidmax DOUBLE: count substitutions only for pairs with PID smaller than this value (default none)
|
73
|
+
--heatmap INTEGER:
|
74
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+
0 create a heat map file for each substitution table
|
75
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+
1 create one big file containing all heat maps from substitution tables
|
76
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+
2 do both 0 and 1
|
77
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+
--heatmap-format INTEGER:
|
78
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+
0 for Portable Network Graphics (PNG) Format (default)
|
79
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+
1 for Graphics Interchange Format (GIF)
|
80
|
+
2 for Joint Photographic Experts Group (JPEG) Format
|
81
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+
3 for Microsoft Windows bitmap (BMP) Format
|
82
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+
4 for Portable Document Format (PDF)
|
83
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+
--heatmap-columns INTEGER: number of tables to print in a row when --heatmap 1 or 2 set (default: sqrt(no. of tables))
|
84
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+
--heatmap-stem STRING: stem for a file name when --heatmap 1 or 2 set (default: 'heatmap')
|
85
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+
--heatmap-values: print values in the cells when generating heat maps
|
57
86
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--verbose (-v) INTEGER
|
58
|
-
0 for ERROR level
|
59
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-
1 for WARN or above level
|
87
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+
0 for ERROR level
|
88
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+
1 for WARN or above level (default)
|
60
89
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2 for INFO or above level
|
61
90
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3 for DEBUG or above level
|
62
91
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--version: print version
|
63
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--help (-h): show help
|
64
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|
65
94
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|
66
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-
==
|
95
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+
== Usage
|
96
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+
|
97
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+
1. Prepare an environmental class definition file. For more details, please check this notes (http://www-cryst.bioc.cam.ac.uk/~kenji/subst/NOTES).
|
98
|
+
|
99
|
+
~user $ cat classdef.dat
|
100
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+
#
|
101
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+
# name of feature (string); values adopted in .tem file (string); class labels assigned for each value (string);
|
102
|
+
# constrained or not (T or F); silent (used as masks)? (T or F)
|
103
|
+
#
|
104
|
+
secondary structure and phi angle;HEPC;HEPC;T;F
|
105
|
+
solvent accessibility;TF;Aa;F;F
|
106
|
+
|
107
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+
2. Prepare structural alignments and their annotations of above environmental classes in PIR format.
|
108
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+
|
109
|
+
~user $ cat sample1.tem
|
110
|
+
>P1;1mnma
|
111
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+
sequence
|
112
|
+
QKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKFEPIVTQQEGRNL
|
113
|
+
IQACLNAPDD*
|
114
|
+
>P1;1egwa
|
115
|
+
sequence
|
116
|
+
--GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEY--
|
117
|
+
----------*
|
118
|
+
>P1;1mnma
|
119
|
+
secondary structure and phi angle
|
120
|
+
CPCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHPCCCEEEEECCCPCEEEEECCCCCHHHHCHHHHHH
|
121
|
+
HHHHHCCCCP*
|
122
|
+
>P1;1egwa
|
123
|
+
secondary structure and phi angle
|
124
|
+
--CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCPCCCEEEEECCCPCEEEEECCCHHHHHHHHHHC--
|
125
|
+
----------*
|
126
|
+
>P1;1mnma
|
127
|
+
solvent accessibility
|
128
|
+
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTFTTTTTTTTTTTTTTTT
|
129
|
+
TTTTTTTTTT*
|
130
|
+
>P1;1egwa
|
131
|
+
solvent accessibility
|
132
|
+
--TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTFTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT--
|
133
|
+
----------*
|
134
|
+
...
|
135
|
+
|
136
|
+
3. When you have two or more alignment files, you should make a separate file containing all the paths for the alignment files.
|
137
|
+
|
138
|
+
~user $ ls -1 *.tem > TEMLIST
|
139
|
+
~user $ cat TEMLIST
|
140
|
+
sample1.tem
|
141
|
+
sample2.tem
|
142
|
+
...
|
143
|
+
|
144
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+
4. To produce substitution count matrices, type
|
145
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+
|
146
|
+
~user $ egor -l TEMLIST --output 0 -o substcount.mat
|
147
|
+
|
148
|
+
5. To produce substitution probability matrices, type
|
149
|
+
|
150
|
+
~user $ egor -l TEMLIST --output 1 -o substprob.mat
|
67
151
|
|
68
|
-
|
69
|
-
* rubygems 1.2.0 or above (http://rubyforge.org/projects/rubygems/)
|
152
|
+
6. To produce log odds ratio matrices, type
|
70
153
|
|
71
|
-
|
154
|
+
~user $ egor -l TEMLIST --output 2 -o substlogo.mat
|
155
|
+
|
156
|
+
7. To produce substitution data only from the sequence pairs within a given PID range, type (if you don't provide any name for output, 'allmat.dat' will be used.)
|
157
|
+
|
158
|
+
~user $ egor -l TEMLIST --pidmin 60 --pidmax 80 --output 1
|
159
|
+
|
160
|
+
8. To change the clustering level (default 60), type
|
161
|
+
|
162
|
+
~user $ egor -l TEMLIST --weight 80 --output 2
|
163
|
+
|
164
|
+
9. In case any positions are masked with the character 'X' in any environmental features will be excluded from the calculation of substitution counts.
|
165
|
+
|
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).
|
167
|
+
|
168
|
+
# Environment-specific amino acid substitution matrices
|
169
|
+
# Creator: egor version 0.0.5
|
170
|
+
# Creation Date: 05/02/2009 17:29
|
171
|
+
#
|
172
|
+
# Definitions for structural environments:
|
173
|
+
# 2 features used
|
174
|
+
#
|
175
|
+
# secondary structure and phi angle;HEPC;HEPC;F;F
|
176
|
+
# solvent accessibility;TF;Aa;F;F
|
177
|
+
# (read in from classdef.dat)
|
178
|
+
#
|
179
|
+
# Number of alignments: 1187
|
180
|
+
# (list of .tem files read in from TEMLIST)
|
181
|
+
#
|
182
|
+
# Total number of environments: 8
|
183
|
+
#
|
184
|
+
# There are 21 amino acids considered.
|
185
|
+
# ACDEFGHIKLMNPQRSTVWYJ
|
186
|
+
#
|
187
|
+
# C: Cystine (the disulfide-bonded form)
|
188
|
+
# J: Cysteine (the free thiol form)
|
189
|
+
#
|
190
|
+
# Weighting scheme: clustering at PID 60 level
|
191
|
+
# ...
|
192
|
+
#
|
193
|
+
>HA 0
|
194
|
+
# A C D E F G H I K L M N P Q R S T V W Y J
|
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-values
|
222
|
+
|
223
|
+
which will look like this,
|
224
|
+
|
225
|
+
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
|
+
http://www-cryst.bioc.cam.ac.uk/~semin/images/myheatmaps.gif
|
234
|
+
|
235
|
+
== Repository
|
236
|
+
|
237
|
+
You can download a pre-built RubyGems package from
|
238
|
+
|
239
|
+
* rubyforge: http://rubyforge.org/projects/egor
|
72
240
|
|
73
|
-
|
74
|
-
* facets (http://facets.rubyforge.org/)
|
75
|
-
* bio (http://bioruby.open-bio.org/)
|
76
|
-
* simple_memoize (http://github.com/JackDanger/simple_memoize/tree/master)
|
241
|
+
or, You can fetch the source from
|
77
242
|
|
243
|
+
* github: http://github.com/semin/egor/tree/master
|
78
244
|
|
79
|
-
== LICENSE:
|
80
245
|
|
81
|
-
|
246
|
+
== Contact
|
82
247
|
|
83
|
-
|
248
|
+
Comments are welcome, please send an email to me (seminlee at gmail dot com).
|
84
249
|
|
85
|
-
Permission is hereby granted, free of charge, to any person obtaining
|
86
|
-
a copy of this software and associated documentation files (the
|
87
|
-
'Software'), to deal in the Software without restriction, including
|
88
|
-
without limitation the rights to use, copy, modify, merge, publish,
|
89
|
-
distribute, sublicense, and/or sell copies of the Software, and to
|
90
|
-
permit persons to whom the Software is furnished to do so, subject to
|
91
|
-
the following conditions:
|
92
250
|
|
93
|
-
|
94
|
-
included in all copies or substantial portions of the Software.
|
251
|
+
== License
|
95
252
|
|
96
|
-
|
97
|
-
|
98
|
-
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
|
99
|
-
IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
|
100
|
-
CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
|
101
|
-
TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
|
102
|
-
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
253
|
+
http://i.creativecommons.org/l/by-nc/2.0/uk/88x31.png
|
254
|
+
This work is licensed under a {Creative Commons Attribution-Noncommercial 2.0 UK: England & Wales License}[http://creativecommons.org/licenses/by-nc/2.0/uk/].
|
data/Rakefile
CHANGED
@@ -5,21 +5,21 @@ require File.dirname(__FILE__) + '/lib/egor'
|
|
5
5
|
# Run 'rake -T' to see list of generated tasks (from gem root directory)
|
6
6
|
$hoe = Hoe.new('egor', Egor::VERSION) do |p|
|
7
7
|
p.developer('Semin Lee', 'seminlee@gmail.com')
|
8
|
-
p.changes
|
9
|
-
p.post_install_message
|
10
|
-
p.rubyforge_name
|
11
|
-
p.extra_deps
|
12
|
-
['narray','>= 0.5.9.5'],
|
13
|
-
['bio',
|
14
|
-
['facets','>= 2.4.5'],
|
15
|
-
['
|
8
|
+
p.changes = p.paragraphs_of("History.txt", 0..1).join("\n\n")
|
9
|
+
p.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
|
10
|
+
p.rubyforge_name = p.name # TODO this is default value
|
11
|
+
p.extra_deps = [
|
12
|
+
['narray', '>= 0.5.9.5'],
|
13
|
+
['bio', '>= 1.2.1'],
|
14
|
+
['facets', '>= 2.4.5'],
|
15
|
+
['rmagick', '>= 2.9.1'],
|
16
16
|
]
|
17
17
|
|
18
18
|
p.extra_dev_deps = [
|
19
19
|
['newgem', ">= #{::Newgem::VERSION}"]
|
20
20
|
]
|
21
21
|
|
22
|
-
p.clean_globs |= %w[**/.DS_Store tmp *.log]
|
22
|
+
p.clean_globs |= %w[**/.DS_Store tmp *.log *.swp]
|
23
23
|
path = (p.rubyforge_name == p.name) ? p.rubyforge_name : "\#{p.rubyforge_name}/\#{p.name}"
|
24
24
|
p.remote_rdoc_dir = File.join(path.gsub(/^#{p.rubyforge_name}\/?/,''), 'rdoc')
|
25
25
|
p.rsync_args = '-av --delete --ignore-errors'
|
data/egor.gemspec
CHANGED
@@ -2,28 +2,26 @@
|
|
2
2
|
|
3
3
|
Gem::Specification.new do |s|
|
4
4
|
s.name = %q{egor}
|
5
|
-
s.version = "0.0
|
5
|
+
s.version = "0.9.0"
|
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.
|
10
|
-
s.date = %q{2008-12-15}
|
9
|
+
s.date = %q{2009-02-13}
|
11
10
|
s.default_executable = %q{egor}
|
12
|
-
s.description = %q{egor
|
11
|
+
s.description = %q{'egor' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
|
13
12
|
s.email = ["seminlee@gmail.com"]
|
14
13
|
s.executables = ["egor"]
|
15
14
|
s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "website/index.txt"]
|
16
|
-
s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/egor", "config/website.yml", "config/website.yml.sample", "egor.gemspec", "lib/egor.rb", "lib/egor/cli.rb", "lib/
|
15
|
+
s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/egor", "config/website.yml", "config/website.yml.sample", "egor.gemspec", "lib/egor.rb", "lib/egor/cli.rb", "lib/egor/environment.rb", "lib/egor/environment_class_hash.rb", "lib/egor/environment_feature.rb", "lib/egor/environment_feature_array.rb", "lib/egor/heatmap_array.rb", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "lib/string_extensions.rb", "script/console", "script/destroy", "script/generate", "script/txt2html", "test/egor/test_cli.rb", "test/egor/test_environment_class_hash.rb", "test/egor/test_environment_feature.rb", "test/test_egor.rb", "test/test_helper.rb", "test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "website/index.html", "website/index.txt", "website/javascripts/rounded_corners_lite.inc.js", "website/stylesheets/screen.css", "website/template.html.erb"]
|
17
16
|
s.has_rdoc = true
|
18
|
-
s.homepage = %q{http://
|
17
|
+
s.homepage = %q{http://www-cryst.bioc.cam.ac.uk/egor}
|
19
18
|
s.post_install_message = %q{PostInstall.txt}
|
20
19
|
s.rdoc_options = ["--main", "README.rdoc"]
|
21
20
|
s.require_paths = ["lib"]
|
22
21
|
s.rubyforge_project = %q{egor}
|
23
22
|
s.rubygems_version = %q{1.3.1}
|
24
|
-
s.
|
25
|
-
s.
|
26
|
-
s.test_files = ["test/test_egor.rb", "test/test_egor_cli.rb", "test/test_enumerable_extensions.rb", "test/test_environment_feature.rb", "test/test_helper.rb", "test/test_nmatrix_extensions.rb"]
|
23
|
+
s.summary = %q{'egor' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
|
24
|
+
s.test_files = ["test/test_string_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_math_extensions.rb", "test/test_helper.rb", "test/test_narray_extensions.rb", "test/egor/test_environment_feature.rb", "test/egor/test_cli.rb", "test/egor/test_environment_class_hash.rb", "test/test_egor.rb"]
|
27
25
|
|
28
26
|
if s.respond_to? :specification_version then
|
29
27
|
current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
|
@@ -33,23 +31,23 @@ Gem::Specification.new do |s|
|
|
33
31
|
s.add_runtime_dependency(%q<narray>, [">= 0.5.9.5"])
|
34
32
|
s.add_runtime_dependency(%q<bio>, [">= 1.2.1"])
|
35
33
|
s.add_runtime_dependency(%q<facets>, [">= 2.4.5"])
|
36
|
-
s.add_runtime_dependency(%q<
|
37
|
-
s.add_development_dependency(%q<newgem>, [">= 1.2.
|
34
|
+
s.add_runtime_dependency(%q<rmagick>, [">= 2.9.1"])
|
35
|
+
s.add_development_dependency(%q<newgem>, [">= 1.2.3"])
|
38
36
|
s.add_development_dependency(%q<hoe>, [">= 1.8.0"])
|
39
37
|
else
|
40
38
|
s.add_dependency(%q<narray>, [">= 0.5.9.5"])
|
41
39
|
s.add_dependency(%q<bio>, [">= 1.2.1"])
|
42
40
|
s.add_dependency(%q<facets>, [">= 2.4.5"])
|
43
|
-
s.add_dependency(%q<
|
44
|
-
s.add_dependency(%q<newgem>, [">= 1.2.
|
41
|
+
s.add_dependency(%q<rmagick>, [">= 2.9.1"])
|
42
|
+
s.add_dependency(%q<newgem>, [">= 1.2.3"])
|
45
43
|
s.add_dependency(%q<hoe>, [">= 1.8.0"])
|
46
44
|
end
|
47
45
|
else
|
48
46
|
s.add_dependency(%q<narray>, [">= 0.5.9.5"])
|
49
47
|
s.add_dependency(%q<bio>, [">= 1.2.1"])
|
50
48
|
s.add_dependency(%q<facets>, [">= 2.4.5"])
|
51
|
-
s.add_dependency(%q<
|
52
|
-
s.add_dependency(%q<newgem>, [">= 1.2.
|
49
|
+
s.add_dependency(%q<rmagick>, [">= 2.9.1"])
|
50
|
+
s.add_dependency(%q<newgem>, [">= 1.2.3"])
|
53
51
|
s.add_dependency(%q<hoe>, [">= 1.8.0"])
|
54
52
|
end
|
55
53
|
end
|