semin-egor 0.9.2 → 0.9.3

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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 @@
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- == 0.9.0 version
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+ == 0.9.0, released 2009-2-13
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- * 5 major enhancement:
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- * --heatmap option has been added to generate heat maps from substitution tables
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- * --heatmap-format option has been added for heat map figure format (PNG, GIF, JPG, BMP, and PDF)
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- * --heatmap-stem option has been added to set a file name for total heat maps figure when --heatmap 1 or 2 is set
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- * --heatmap-columns option has been added to set the number of tables in a row when --heatmap 1 or 2 is set
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- * --heatmap-value option has been added to print values in the cells of heat maps
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+ * Added --heatmap option for heat map generation from substitution tables
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+ * Added --heatmap-format option for heat map figure format (PNG, GIF, JPG, BMP, and PDF)
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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
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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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+ * Added --heatmap-value option to print values in the cells of heat maps
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+ * Renamed --noround option to --noroundoff
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+ * 'simple_memoize' RubyGem package is no longer required
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- * 2 minor enhancement:
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- * --noround option has been renamed to --noroundoff
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- * 'simple_memoize' RubyGem package is no longer required
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+ == 0.0.5, released 2009-1-23
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- == 0.0.5 2009-1-23
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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)
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+ * Added --augosigma option to avoid excessive influence of background frequencies
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+ * Added --noround option was added to get original log odds ratios
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+ * Added --p1smooth option was added to enable p1 probability smoothing when partial smoothing
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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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- * 4 major enhancement:
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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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- * --augosigma option was added to avoid excessive influence of background frequencies
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- * a bug in p2 probability 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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+ == 0.0.4, released 2008-12-15
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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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-
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- == 0.0.4 2008-12-15
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-
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- * 2 major enhancement:
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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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+ * 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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  == 0.0.3 2008-12-09
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- * 2 major enhancement:
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- * An option '--cys (-j) 2' added not to distinguish J from C, so 'disulphide bond' environment feature is not prerequisite
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- * Masking works for target amino acid, too
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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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- == 0.0.2 2008-11-13
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+ == 0.0.2, released 2008-11-13
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- * 2 major enhancement:
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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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+ * Supports user provided constrained environment features are properly handled
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- == 0.0.1 2008-11-07
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+ == 0.0.1, released 2008-11-07
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- * 1 major enhancement:
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- * Initial release
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+ * 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
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  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").
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- #
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  # Environment-specific amino acid substitution matrices
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- # Creator: egor version 0.0.4
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- # Creation Date: 20/01/2009 14:45
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+ # Creator: egor version 0.0.5
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+ # Creation Date: 05/02/2009 17:29
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  #
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  # Definitions for structural environments:
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- # 5 features used
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+ # 2 features used
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  #
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  # secondary structure and phi angle;HEPC;HEPC;F;F
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  # solvent accessibility;TF;Aa;F;F
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- # hydrogen bond to DNA;TF;Hh;F;F
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- # water-mediated hydrogen bond to DNA;TF;Ww;F;F
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- # van der Waals contact to DNA;TF;Vv;F;F
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- #
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  # (read in from classdef.dat)
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  #
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- # Number of alignments: 86
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+ # Number of alignments: 1187
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  # (list of .tem files read in from TEMLIST)
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  #
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- # Total number of environments: 64
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+ # Total number of environments: 8
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  #
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  # There are 21 amino acids considered.
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  # ACDEFGHIKLMNPQRSTVWYJ
@@ -193,34 +188,49 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
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  # J: Cysteine (the free thiol form)
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  #
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  # Weighting scheme: clustering at PID 60 level
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- #
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  # ...
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  #
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- >HAHWV 0
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+ >HA 0
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  # A C D E F G H I K L M N P Q R S T V W Y J
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- A 5 -6 0 0 -2 0 -2 -1 -1 -1 1 -1 -1 0 -1 1 0 0 -2 -2 -2
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- C -7 28 -8 -49 -3 -49 -2 -1 -11 -5 -1 -49 -6 -49 -49 -4 -6 -4 -49 3 9
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- D 0 -7 7 2 -3 0 0 -4 0 -3 -3 2 0 0 -2 1 0 -3 -5 -3 -6
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- E 0 -68 2 5 -3 -1 -1 -3 0 -3 -1 0 0 1 -1 0 0 -3 -3 -2 -7
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- F -2 -3 -3 -4 8 -4 -1 2 -4 1 0 -4 -4 -4 -4 -4 -2 1 2 3 -5
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- G 0 -67 0 -1 -4 9 -3 -4 -2 -3 -4 1 -1 -2 -3 0 -2 -3 -3 -3 -2
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- H -2 -2 0 -1 -1 -3 11 -3 -2 -3 -2 0 -2 -1 -1 -1 -1 -3 -2 0 -4
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- I -1 -1 -4 -3 2 -4 -3 6 -3 2 2 -4 -2 -2 -4 -3 -1 3 -1 0 -4
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- K -1 -10 0 0 -4 -2 -1 -3 5 -3 -2 0 0 1 2 -1 -1 -3 -4 -2 -5
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- L -1 -5 -3 -3 1 -3 -3 2 -3 5 2 -4 -1 -2 -2 -3 -1 1 0 -1 -4
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- M 1 -1 -3 -1 0 -4 -2 2 -3 2 8 -2 -2 -1 -2 -2 -1 1 -1 -1 -4
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- N -1 -66 2 0 -4 1 0 -4 0 -4 -2 8 -1 0 -1 1 0 -3 -5 -4 -5
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- P -1 -6 0 0 -3 -1 -2 -2 -1 -1 -2 -1 9 -1 -2 0 0 -2 -4 -3 -7
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- Q 0 -66 0 1 -4 -2 -1 -2 1 -2 -1 0 -1 6 0 0 -1 -2 -2 -2 -6
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- R -1 -69 -1 0 -4 -3 -1 -3 2 -2 -1 -1 -2 0 6 -1 -1 -3 -3 -2 -6
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- S 1 -4 1 0 -3 0 -1 -3 -1 -3 -2 1 0 0 -1 5 2 -2 -3 -1 -3
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- T 0 -5 -1 -1 -2 -2 -1 -1 -1 -1 -1 0 0 -1 -1 2 5 -1 -3 -2 -3
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- V 0 -4 -3 -3 1 -4 -3 3 -3 1 1 -3 -2 -2 -3 -2 -1 6 0 -1 -2
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- W -2 -61 -5 -3 2 -3 -2 -1 -4 0 -1 -5 -4 -2 -3 -3 -3 0 14 3 -6
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- Y -2 3 -3 -2 4 -3 0 0 -2 0 0 -4 -3 -2 -2 -1 -2 0 3 9 -3
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- J -3 9 -7 -8 -5 -2 -4 -4 -6 -4 -4 -5 -7 -6 -6 -3 -3 -2 -6 -3 15
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- U -3 15 -7 -8 -5 -3 -4 -4 -6 -4 -4 -5 -7 -6 -6 -3 -3 -2 -6 -3 15
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- ...
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+ A 3 -5 0 0 -1 2 0 0 1 0 0 0 1 1 0 1 1 1 -1 0 2
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+ C -16 19 -16 -18 -11 -14 -13 -13 -14 -14 -14 -11 -17 -16 -13 -16 -14 -12 -12 -10 -4
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+ D 1 -7 6 3 -3 1 0 -3 1 -3 -2 2 1 2 0 1 0 -2 -3 -2 -2
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+ E 3 -7 5 7 -1 2 2 0 3 0 0 3 2 4 3 3 2 1 -1 0 -1
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+ F -4 -4 -6 -6 7 -5 -1 0 -4 1 0 -5 -5 -4 -4 -4 -3 -1 3 3 0
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+ G -2 -6 -3 -4 -5 5 -4 -5 -4 -5 -4 -2 -3 -4 -4 -2 -3 -5 -6 -4 -3
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+ H 0 -6 0 0 1 0 8 -1 0 0 0 1 -2 1 1 0 0 0 1 3 0
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+ I -3 -7 -6 -5 0 -5 -3 4 -4 1 1 -5 -4 -4 -3 -5 -2 2 -2 -1 0
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+ K 2 -6 2 2 -1 1 2 0 5 1 1 2 0 3 4 2 2 0 -2 0 -1
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+ L -2 -6 -5 -4 1 -4 -2 2 -3 4 2 -3 -4 -3 -2 -4 -2 1 0 0 1
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+ M -2 -7 -4 -3 1 -2 -1 2 -2 2 6 -3 -4 -2 -1 -2 -1 1 0 0 1
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+ N 0 -5 1 0 -3 1 1 -3 0 -2 -2 6 -2 0 0 1 1 -2 -3 -1 -1
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+ P -1 -7 -1 -2 -4 -1 -3 -3 -2 -3 -4 -2 9 -2 -3 0 -1 -2 -4 -4 -4
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+ Q 2 -7 2 2 -1 1 2 -1 2 0 0 2 0 5 2 1 1 0 -2 -1 0
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+ R 1 -6 1 1 -1 0 2 0 3 0 1 1 -1 2 6 1 1 0 -1 0 0
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+ S 0 -6 -1 -1 -3 0 -2 -3 -1 -3 -3 0 0 -1 -1 3 1 -2 -4 -3 0
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+ T -1 -7 -2 -2 -3 -2 -2 -2 -2 -2 -2 -1 -2 -2 -2 0 3 -1 -3 -3 0
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+ V -3 -6 -6 -5 -1 -4 -3 1 -4 0 0 -5 -3 -4 -4 -4 -2 2 -2 -2 0
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+ W -4 -6 -6 -5 2 -6 -2 -2 -5 -1 -2 -5 -5 -4 -4 -5 -4 -2 12 2 -3
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+ Y -3 -5 -5 -5 3 -4 1 -1 -3 -1 -1 -3 -5 -3 -3 -4 -3 -2 3 7 -1
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+ J -2 0 -4 -5 0 -2 -1 0 -3 0 0 -3 -6 -2 -2 -1 -1 0 -1 0 9
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+ U -5 16 -7 -8 -3 -5 -4 -3 -6 -3 -3 -5 -9 -6 -5 -4 -4 -3 -4 -3 6
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+ ...
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+
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+ 11. To generate a heat map for each table with values in it,
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+
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+ ~user $ egor -l TEMLIST --heatmap 0 --heatmap-value
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+
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+ which will look like this,
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+ <img alt="Sample Heat Map" style="border-width:0" src="http://www-cryst.bioc.cam.ac.uk/~semin/images/0. HA.png">
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+ 12. To generate one big figure, 'myheatmaps.gif' containing all the heat maps (4 maps in a row),
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+ ~user $ egor -l TEMLIST --heatmap 1 --heatmap-stem myheatmaps --heatmap-format 1 --heatmap-columns 4
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+ which will look like this,
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+ <img alt="Sample Heat Maps" style="border-width:0" src="http://www-cryst.bioc.cam.ac.uk/~semin/images/myheatmaps.gif">
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  ## Repository
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data/egor.gemspec CHANGED
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  Gem::Specification.new do |s|
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  s.name = %q{egor}
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- s.version = "0.9.2"
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+ s.version = "0.9.3"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = ["Semin Lee"]
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- s.date = %q{2009-02-12}
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+ s.date = %q{2009-02-13}
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  s.default_executable = %q{egor}
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  s.email = ["seminlee@gmail.com"]
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  s.executables = ["egor"]
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  s.require_paths = ["lib"]
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  s.rubyforge_project = %q{egor}
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  s.rubygems_version = %q{1.3.1}
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- s.summary = "A new ESST generator"
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+ s.summary = 'A new ESST generator'
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  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"]
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  if s.respond_to? :specification_version then
data/lib/egor.rb CHANGED
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  $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
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  module Egor
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- VERSION = '0.9.2'
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+ VERSION = '0.9.3'
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  end
metadata CHANGED
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  --- !ruby/object:Gem::Specification
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  name: semin-egor
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  version: !ruby/object:Gem::Version
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- version: 0.9.2
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+ version: 0.9.3
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  platform: ruby
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  authors:
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  - Semin Lee
@@ -9,7 +9,7 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2009-02-12 00:00:00 -08:00
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+ date: 2009-02-13 00:00:00 -08:00
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  default_executable: egor
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  dependencies:
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  - !ruby/object:Gem::Dependency