semin-egor 0.9.1 → 0.9.2

data/README.markdown

@@ -0,0 +1,243 @@
+# egor
+
+[http://www-cryst.bioc.cam.ac.uk/egor](http://www-cryst.bioc.cam.ac.uk/egor "Egor Homepage")
+
+
+## Description
+
+'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.
+
+
+## Features
+
+* Environment-specific substitution table generation based on user providing environmental class definition
+* Entropy-based smoothing procedures to cope with sparse data problem
+* BLOSUM-like weighting procedures using PID threshold
+* Heat Map generation for substitution tables
+
+
+## Requirements
+
+* ruby 1.8.7 or above ([http://www.ruby-lang.org](http://www.ruby-lang.org "Ruby"))
+* rubygems 1.2.0 or above ([http://rubyforge.org/projects/rubygems/](http://rubyforge.org/projects/rubygems "RubyGems"))
+
+Following RubyGems will be automatically installed if you have rubygems installed on your machine
+
+* narray ([http://narray.rubyforge.org](http://narray.rubyforge.org "NArray"))
+* facets ([http://facets.rubyforge.org](http://facets.rubyforge.org "Ruby Facets"))
+* bio ([http://bioruby.open-bio.org](http://bioruby.open-bio.org "BioRuby"))
+* RMagick ([http://rmagick.rubyforge.org/](http://rmagick.rubyforge.org/ "RMagick"))
+
+
+## Installation
+
+    ~user $ sudo gem install egor
+
+
+## Basic Usage
+
+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'.
+
+    ~user $ egor -l TEMLIST-file -c classdef.dat
+                or
+    ~user $ egor -f TEM-file -c classdef.dat
+
+
+## Options
+    --tem-file (-f) FILE: a tem file
+    --tem-list (-l) FILE: a list for tem files
+    --classdef (-c) FILE: a file for the defintion of environments (default: 'classdef.dat')
+    --outfile (-o) FILE: output filename (default 'allmat.dat')
+    --weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting (default: 60)
+    --noweight: calculate substitution count with no weights
+    --smooth (-s) INTEGER:
+        0 for partial smoothing (default)
+        1 for full smoothing
+    --p1smooth: perform smoothing for p1 probability calculation when partial smoothing
+    --nosmooth: perform no smoothing operation
+    --cys (-y) INTEGER:
+        0 for using C and J only for structure (default)
+        1 for both structure and sequence
+        2 for using only C for both (must be set when you have no 'disulphide' or 'disulfide' annotation in templates)
+    --output INTEGER:
+        0 for raw count (no smoothing performed)
+        1 for probabilities
+        2 for log odds ratios (default)
+    --noroundoff: do not round off log odds ratio
+    --scale INTEGER: log odds ratio matrices in 1/n bit units (default 3)
+    --sigma DOUBLE: change the sigma value for smoothing (default 5.0)
+    --autosigma: automatically adjust the sigma value for smoothing
+    --add DOUBLE: add this value to raw count when deriving log odds ratios without smoothing (default 1/#classes)
+    --pidmin DOUBLE: count substitutions only for pairs with PID equal to or greater than this value (default none)
+    --pidmax DOUBLE: count substitutions only for pairs with PID smaller than this value (default none)
+    --heatmap INTEGER:
+        0 create a heat map file for each substitution table
+        1 create one big file containing all heat maps from substitution tables
+        2 do both 0 and 1
+    --heatmap-format INTEGER:
+        0 for Portable Network Graphics (PNG) Format (default)
+        1 for Graphics Interchange Format (GIF)
+        2 for Joint Photographic Experts Group (JPEG) Format
+        3 for Microsoft Windows bitmap (BMP) Format
+        4 for Portable Document Format (PDF)
+    --heatmap-columns INTEGER: number of tables to print in a row when --heatmap 1 or 2 set (default: sqrt(no. of tables))
+    --heatmap-stem STRING: stem for a file name when --heatmap 1 or 2 set (default: 'heatmap')
+    --heatmap-value: print values in the cells when generating heat maps
+    --verbose (-v) INTEGER
+        0 for ERROR level
+        1 for WARN or above level (default)
+        2 for INFO or above level
+        3 for DEBUG or above level
+    --version: print version
+    --help (-h): show help
+
+
+## Usage
+
+1. Prepare an environmental class definition file. For more details, please check this [notes](http://www-cryst.bioc.cam.ac.uk/~kenji/subst/NOTES "Kenji's NOTES").
+
+        ~user $ cat classdef.dat
+        #
+        # name of feature (string); values adopted in .tem file (string); class labels assigned for each value (string);
+        # constrained or not (T or F); silent (used as masks)? (T or F)
+        #
+        secondary structure and phi angle;HEPC;HEPC;T;F
+        solvent accessibility;TF;Aa;F;F
+
+2. Prepare structural alignments and their annotations of above environmental classes in [PIR format](http://caps.ncbs.res.in/gendis/pir.html "PIR Format").
+
+        ~user $ cat sample1.tem
+        >P1;1mnma
+        sequence
+        QKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKFEPIVTQQEGRNL
+        IQACLNAPDD*
+        >P1;1egwa
+        sequence
+        --GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEY--
+        ----------*
+        >P1;1mnma
+        secondary structure and phi angle
+        CPCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHPCCCEEEEECCCPCEEEEECCCCCHHHHCHHHHHH
+        HHHHHCCCCP*
+        >P1;1egwa
+        secondary structure and phi angle
+        --CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCPCCCEEEEECCCPCEEEEECCCHHHHHHHHHHC--
+        ----------*
+        >P1;1mnma
+        solvent accessibility
+        TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTFTTTTTTTTTTTTTTTT
+        TTTTTTTTTT*
+        >P1;1egwa
+        solvent accessibility
+        --TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTFTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT--
+        ----------*
+        ... 
+
+3. When you have two or more alignment files, you should make a separate file containing all the paths for the alignment files.
+
+        ~user $ ls -1 *.tem > TEMLIST
+        ~user $ cat TEMLIST
+        sample1.tem
+        sample2.tem
+        ...
+
+4. To produce substitution count matrices, type
+
+        ~user $ egor -l TEMLIST --output 0 -o substcount.mat
+
+5. To produce substitution probability matrices, type
+
+        ~user $ egor -l TEMLIST --output 1 -o substprob.mat
+
+6. To produce log odds ratio matrices, type
+
+        ~user $ egor -l TEMLIST --output 2 -o substlogo.mat
+
+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.)
+
+        ~user $ egor -l TEMLIST --pidmin 60 --pidmax 80 --output 1
+
+8. To change the clustering level (default 60), type
+
+        ~user $ egor -l TEMLIST --weight 80 --output 2
+
+9. In case any positions are masked with the character 'X' in any environmental features will be excluded from the calculation of substitution counts.
+
+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").
+
+        #
+        # Environment-specific amino acid substitution matrices
+        # Creator: egor version 0.0.4
+        # Creation Date: 20/01/2009 14:45
+        #
+        # Definitions for structural environments:
+        # 5 features used
+        #
+        # secondary structure and phi angle;HEPC;HEPC;F;F
+        # solvent accessibility;TF;Aa;F;F
+        # hydrogen bond to DNA;TF;Hh;F;F
+        # water-mediated hydrogen bond to DNA;TF;Ww;F;F
+        # van der Waals contact to DNA;TF;Vv;F;F
+        #
+        # (read in from classdef.dat)
+        #
+        # Number of alignments: 86
+        # (list of .tem files read in from TEMLIST)
+        #
+        # Total number of environments: 64
+        #
+        # There are 21 amino acids considered.
+        # ACDEFGHIKLMNPQRSTVWYJ
+        # 
+        # C: Cystine (the disulfide-bonded form)
+        # J: Cysteine (the free thiol form)
+        #
+        # Weighting scheme: clustering at PID 60 level
+        #
+        # ...
+        #
+        >HAHWV 0
+        #        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y      J
+        A        5     -6      0      0     -2      0     -2     -1     -1     -1      1     -1     -1      0     -1      1      0      0     -2     -2     -2
+        C       -7     28     -8    -49     -3    -49     -2     -1    -11     -5     -1    -49     -6    -49    -49     -4     -6     -4    -49      3      9
+        D        0     -7      7      2     -3      0      0     -4      0     -3     -3      2      0      0     -2      1      0     -3     -5     -3     -6
+        E        0    -68      2      5     -3     -1     -1     -3      0     -3     -1      0      0      1     -1      0      0     -3     -3     -2     -7
+        F       -2     -3     -3     -4      8     -4     -1      2     -4      1      0     -4     -4     -4     -4     -4     -2      1      2      3     -5
+        G        0    -67      0     -1     -4      9     -3     -4     -2     -3     -4      1     -1     -2     -3      0     -2     -3     -3     -3     -2
+        H       -2     -2      0     -1     -1     -3     11     -3     -2     -3     -2      0     -2     -1     -1     -1     -1     -3     -2      0     -4
+        I       -1     -1     -4     -3      2     -4     -3      6     -3      2      2     -4     -2     -2     -4     -3     -1      3     -1      0     -4
+        K       -1    -10      0      0     -4     -2     -1     -3      5     -3     -2      0      0      1      2     -1     -1     -3     -4     -2     -5
+        L       -1     -5     -3     -3      1     -3     -3      2     -3      5      2     -4     -1     -2     -2     -3     -1      1      0     -1     -4
+        M        1     -1     -3     -1      0     -4     -2      2     -3      2      8     -2     -2     -1     -2     -2     -1      1     -1     -1     -4
+        N       -1    -66      2      0     -4      1      0     -4      0     -4     -2      8     -1      0     -1      1      0     -3     -5     -4     -5
+        P       -1     -6      0      0     -3     -1     -2     -2     -1     -1     -2     -1      9     -1     -2      0      0     -2     -4     -3     -7
+        Q        0    -66      0      1     -4     -2     -1     -2      1     -2     -1      0     -1      6      0      0     -1     -2     -2     -2     -6
+        R       -1    -69     -1      0     -4     -3     -1     -3      2     -2     -1     -1     -2      0      6     -1     -1     -3     -3     -2     -6
+        S        1     -4      1      0     -3      0     -1     -3     -1     -3     -2      1      0      0     -1      5      2     -2     -3     -1     -3
+        T        0     -5     -1     -1     -2     -2     -1     -1     -1     -1     -1      0      0     -1     -1      2      5     -1     -3     -2     -3
+        V        0     -4     -3     -3      1     -4     -3      3     -3      1      1     -3     -2     -2     -3     -2     -1      6      0     -1     -2
+        W       -2    -61     -5     -3      2     -3     -2     -1     -4      0     -1     -5     -4     -2     -3     -3     -3      0     14      3     -6
+        Y       -2      3     -3     -2      4     -3      0      0     -2      0      0     -4     -3     -2     -2     -1     -2      0      3      9     -3
+        J       -3      9     -7     -8     -5     -2     -4     -4     -6     -4     -4     -5     -7     -6     -6     -3     -3     -2     -6     -3     15
+        U       -3     15     -7     -8     -5     -3     -4     -4     -6     -4     -4     -5     -7     -6     -6     -3     -3     -2     -6     -3     15
+        ... 
+
+## Repository
+
+You can download a pre-built RubyGems package from
+
+* rubyforge: [http://rubyforge.org/projects/egor](http://rubyforge.org/projects/egor "RubyForge")
+
+or, You can fetch the source from
+
+* github: [http://github.com/semin/egor/tree/master](http://github.com/semin/egor/tree/master "GitHub")
+
+
+## Contact
+
+Comments are welcome, please send an email to me (seminlee at gmail dot com). 
+
+
+## License
+
+<a rel="license" href="http://creativecommons.org/licenses/by-nc/2.0/uk/"><img alt="Creative Commons License" style="border-width:0" src="http://i.creativecommons.org/l/by-nc/2.0/uk/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc/2.0/uk/">Creative Commons Attribution-Noncommercial 2.0 UK: England &amp; Wales License</a>.

data/egor.gemspec

@@ -2,7 +2,7 @@
 
 Gem::Specification.new do |s|
   s.name = %q{egor}
-  s.version = "0.9.1"
+  s.version = "0.9.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Semin Lee"]
@@ -11,7 +11,7 @@ Gem::Specification.new do |s|
   s.email = ["seminlee@gmail.com"]
   s.executables = ["egor"]
   s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "website/index.txt"]
-  s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "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/test_egor.rb", "test/test_egor_cli.rb", "test/test_egor_environment_class_hash.rb", "test/test_egor_environment_feature.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"]
+  s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.markdown", "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/test_egor.rb", "test/test_egor_cli.rb", "test/test_egor_environment_class_hash.rb", "test/test_egor_environment_feature.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"]
   s.has_rdoc = true
   s.post_install_message = %q{PostInstall.txt}
   s.rdoc_options = ["--main", "README.markdown"]

data/lib/egor/cli.rb

@@ -72,7 +72,7 @@ Options:
     --pidmax DOUBLE: count substitutions only for pairs with PID smaller than this value (default none)
     --heatmap INTEGER:
         0 create a heat map file for each substitution table
-        1 create one big file containing all substitution tables
+        1 create one big file containing all heat maps from substitution tables
         2 do both 0 and 1
     --heatmap-format INTEGER:
         0 for Portable Network Graphics (PNG) Format (default)

data/lib/egor.rb

@@ -2,5 +2,5 @@ $:.unshift(File.dirname(__FILE__)) unless
   $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
 
 module Egor
-  VERSION = '0.9.1'
+  VERSION = '0.9.2'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: semin-egor
 version: !ruby/object:Gem::Version 
-  version: 0.9.1
+  version: 0.9.2
 platform: ruby
 authors: 
 - Semin Lee
@@ -82,6 +82,7 @@ files:
 - History.txt
 - Manifest.txt
 - PostInstall.txt
+- README.markdown
 - Rakefile
 - bin/egor
 - config/website.yml