semin-egor 0.9.1 → 0.9.2

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Files changed (5) hide show
  1. data/README.markdown +243 -0
  2. data/egor.gemspec +2 -2
  3. data/lib/egor/cli.rb +1 -1
  4. data/lib/egor.rb +1 -1
  5. metadata +2 -1
data/README.markdown ADDED
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+ # egor
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+
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+ [http://www-cryst.bioc.cam.ac.uk/egor](http://www-cryst.bioc.cam.ac.uk/egor "Egor Homepage")
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+
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+
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+ ## Description
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+
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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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+
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+
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+ ## Features
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+
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+ * Environment-specific substitution table generation based on user providing environmental class definition
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+ * Entropy-based smoothing procedures to cope with sparse data problem
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+ * BLOSUM-like weighting procedures using PID threshold
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+ * Heat Map generation for substitution tables
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+
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+
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+ ## Requirements
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+
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+ * ruby 1.8.7 or above ([http://www.ruby-lang.org](http://www.ruby-lang.org "Ruby"))
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+ * rubygems 1.2.0 or above ([http://rubyforge.org/projects/rubygems/](http://rubyforge.org/projects/rubygems "RubyGems"))
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+
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+ Following RubyGems will be automatically installed if you have rubygems installed on your machine
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+
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+ * narray ([http://narray.rubyforge.org](http://narray.rubyforge.org "NArray"))
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+ * facets ([http://facets.rubyforge.org](http://facets.rubyforge.org "Ruby Facets"))
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+ * bio ([http://bioruby.open-bio.org](http://bioruby.open-bio.org "BioRuby"))
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+ * RMagick ([http://rmagick.rubyforge.org/](http://rmagick.rubyforge.org/ "RMagick"))
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+
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+
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+ ## Installation
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+
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+ ~user $ sudo gem install egor
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+
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+
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+ ## Basic Usage
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+
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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'.
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+
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+ ~user $ egor -l TEMLIST-file -c classdef.dat
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+ or
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+ ~user $ egor -f TEM-file -c classdef.dat
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+
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+
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+ ## Options
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+ --tem-file (-f) FILE: a tem file
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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 (default: 60)
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+ --noweight: calculate substitution count with no weights
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+ --smooth (-s) INTEGER:
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+ 0 for partial smoothing (default)
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+ 1 for full smoothing
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+ --p1smooth: perform smoothing for p1 probability calculation when partial smoothing
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+ --nosmooth: perform no smoothing operation
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+ --cys (-y) INTEGER:
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+ 0 for using C and J only for structure (default)
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+ 1 for both structure and sequence
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+ 2 for using only C for both (must be set when you have no 'disulphide' or 'disulfide' annotation in templates)
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+ --output INTEGER:
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+ 0 for raw count (no smoothing performed)
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+ 1 for probabilities
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+ 2 for log odds ratios (default)
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+ --noroundoff: do not round off log odds ratio
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+ --scale INTEGER: log odds ratio matrices in 1/n bit units (default 3)
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+ --sigma DOUBLE: change the sigma value for smoothing (default 5.0)
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+ --autosigma: automatically adjust the sigma value for smoothing
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+ --add DOUBLE: add this value to raw count when deriving log odds ratios without smoothing (default 1/#classes)
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+ --pidmin DOUBLE: count substitutions only for pairs with PID equal to or greater than this value (default none)
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+ --pidmax DOUBLE: count substitutions only for pairs with PID smaller than this value (default none)
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+ --heatmap INTEGER:
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+ 0 create a heat map file for each substitution table
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+ 1 create one big file containing all heat maps from substitution tables
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+ 2 do both 0 and 1
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+ --heatmap-format INTEGER:
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+ 0 for Portable Network Graphics (PNG) Format (default)
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+ 1 for Graphics Interchange Format (GIF)
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+ 2 for Joint Photographic Experts Group (JPEG) Format
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+ 3 for Microsoft Windows bitmap (BMP) Format
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+ 4 for Portable Document Format (PDF)
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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))
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+ --heatmap-stem STRING: stem for a file name when --heatmap 1 or 2 set (default: 'heatmap')
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+ --heatmap-value: print values in the cells when generating heat maps
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+ --verbose (-v) INTEGER
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+ 0 for ERROR level
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+ 1 for WARN or above level (default)
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+ 2 for INFO or above level
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+ 3 for DEBUG or above level
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+ --version: print version
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+ --help (-h): show help
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+
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+
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+ ## Usage
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+
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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 "Kenji's NOTES").
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+
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+ ~user $ cat classdef.dat
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+ #
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+ # name of feature (string); values adopted in .tem file (string); class labels assigned for each value (string);
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+ # constrained or not (T or F); silent (used as masks)? (T or F)
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+ #
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+ secondary structure and phi angle;HEPC;HEPC;T;F
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+ solvent accessibility;TF;Aa;F;F
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+
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+ 2. Prepare structural alignments and their annotations of above environmental classes in [PIR format](http://caps.ncbs.res.in/gendis/pir.html "PIR Format").
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+
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+ ~user $ cat sample1.tem
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+ >P1;1mnma
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+ sequence
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+ QKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKFEPIVTQQEGRNL
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+ IQACLNAPDD*
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+ >P1;1egwa
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+ sequence
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+ --GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEY--
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+ ----------*
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+ >P1;1mnma
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+ secondary structure and phi angle
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+ CPCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHPCCCEEEEECCCPCEEEEECCCCCHHHHCHHHHHH
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+ HHHHHCCCCP*
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+ >P1;1egwa
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+ secondary structure and phi angle
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+ --CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCPCCCEEEEECCCPCEEEEECCCHHHHHHHHHHC--
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+ ----------*
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+ >P1;1mnma
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+ solvent accessibility
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+ TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTFTTTTTTTTTTTTTTTT
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+ TTTTTTTTTT*
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+ >P1;1egwa
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+ solvent accessibility
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+ --TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTFTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT--
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+ ----------*
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+ ...
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+
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+ 3. When you have two or more alignment files, you should make a separate file containing all the paths for the alignment files.
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+
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+ ~user $ ls -1 *.tem > TEMLIST
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+ ~user $ cat TEMLIST
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+ sample1.tem
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+ sample2.tem
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+ ...
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+
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+ 4. To produce substitution count matrices, type
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+ ~user $ egor -l TEMLIST --output 0 -o substcount.mat
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+
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+ 5. To produce substitution probability matrices, type
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+ ~user $ egor -l TEMLIST --output 1 -o substprob.mat
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+
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+ 6. To produce log odds ratio matrices, type
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+ ~user $ egor -l TEMLIST --output 2 -o substlogo.mat
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+
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+ 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.)
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+
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+ ~user $ egor -l TEMLIST --pidmin 60 --pidmax 80 --output 1
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+
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+ 8. To change the clustering level (default 60), type
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+ ~user $ egor -l TEMLIST --weight 80 --output 2
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+
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+ 9. In case any positions are masked with the character 'X' in any environmental features will be excluded from the calculation of substitution counts.
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+
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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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+ #
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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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+ #
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+ # Definitions for structural environments:
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+ # 5 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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+ # (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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+ #
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+ # There are 21 amino acids considered.
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+ # ACDEFGHIKLMNPQRSTVWYJ
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+ #
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+ # C: Cystine (the disulfide-bonded form)
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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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+ # 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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+
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+ ## Repository
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+
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+ You can download a pre-built RubyGems package from
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+
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+ * rubyforge: [http://rubyforge.org/projects/egor](http://rubyforge.org/projects/egor "RubyForge")
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+
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+ or, You can fetch the source from
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+ * github: [http://github.com/semin/egor/tree/master](http://github.com/semin/egor/tree/master "GitHub")
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+
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+
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+ ## Contact
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+ Comments are welcome, please send an email to me (seminlee at gmail dot com).
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+
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+
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+ ## License
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+
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+ <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 CHANGED
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  Gem::Specification.new do |s|
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  s.name = %q{egor}
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- s.version = "0.9.1"
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+ s.version = "0.9.2"
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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.email = ["seminlee@gmail.com"]
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  s.executables = ["egor"]
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  s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "website/index.txt"]
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- 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"]
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+ 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"]
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  s.has_rdoc = true
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  s.post_install_message = %q{PostInstall.txt}
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  s.rdoc_options = ["--main", "README.markdown"]
data/lib/egor/cli.rb CHANGED
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  --pidmax DOUBLE: count substitutions only for pairs with PID smaller than this value (default none)
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  --heatmap INTEGER:
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  0 create a heat map file for each substitution table
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- 1 create one big file containing all substitution tables
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+ 1 create one big file containing all heat maps from substitution tables
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  2 do both 0 and 1
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  --heatmap-format INTEGER:
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  0 for Portable Network Graphics (PNG) Format (default)
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 = '0.9.1'
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+ VERSION = '0.9.2'
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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: 0.9.1
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+ version: 0.9.2
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  platform: ruby
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  authors:
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  - Semin Lee
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  - History.txt
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  - Manifest.txt
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  - PostInstall.txt
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+ - README.markdown
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  - Rakefile
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  - bin/egor
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  - config/website.yml