macroape 3.3.6 → 3.3.7

data/.gitignore

@@ -1,18 +1,18 @@
-*.gem
-*.rbc
-.bundle
-.config
-.yardoc
-Gemfile.lock
-InstalledFiles
-_yardoc
-coverage
-doc/
-lib/bundler/man
-pkg
-rdoc
-spec/reports
-test/tmp
-test/version_tmp
-tmp
-benchmark/
+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+benchmark/*.log

data/Gemfile

@@ -1,4 +1,4 @@
-source 'https://rubygems.org'
-
-# Specify your gem's dependencies in macroape.gemspec
-gemspec
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in macroape.gemspec
+gemspec

data/LICENSE

@@ -1,22 +1,22 @@
-Copyright (c) 2011-2012 Ilya Vorontsov, Ivan Kulakovskiy, Vsevolod Makeev
-
-MIT License
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+Copyright (c) 2011-2012 Ilya Vorontsov, Ivan Kulakovskiy, Vsevolod Makeev
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

@@ -1,68 +1,70 @@
-# Macroape
-
-Macroape is abbreviation for MAtrix CompaRisOn by Approximate P-value Estimation. It's a bioinformatic tool for evaluating similarity measure between a pair of Position Weight Matrices. Used approach and application described in manual at https://docs.google.com/document/pub?id=1_jsxhMNzMzy4d2d_byAd3n6Szg5gEcqG_Sf7w9tEqWw
-
-## Installation
-
-Add this line to your application's Gemfile:
-
-    gem 'macroape'
-
-And then execute:
-
-    $ bundle
-
-Or install it yourself as:
-
-    $ gem install macroape
-
-## Usage
-  For more information read manual at https://docs.google.com/document/pub?id=1_jsxhMNzMzy4d2d_byAd3n6Szg5gEcqG_Sf7w9tEqWw (not last version but comprehensive description of approach)
-
-## Basic usage as a command-line tool
-  MacroAPE have 7 command line tools:
-  
-### Tools for calculating thresholds and pvalues:
-  * find_threshold \<PWM file\> [-p \<pvalue\> (by default: 0.0005)]
-  * find_pvalue \<PWM file\> \<threshold\>
-  
-### Tools for evaluating Jaccard similarity measure in the best alignment and in certain alignment:
-  * eval_similarity \<first PWM file\> \<second PWM file\>
-  * eval_alignment \<first PWM file\> \<second PWM file\> \<shift of second matrix\> \<orientation of second matrix(direct|revcomp)\>
-  
-### Tools for looking through collection for the motifs most similar to a query motif
-  * preprocess_collection \<folder with motif files\> [-o \<collection output file\>]
-  * scan_collection \<query PWM file\> \<collection file\>
-  
-### Tool for finding mutual alignment of several motifs relative to first(leader) motif. It's designed to use with sequence_logo to draw logos of clusters
-  * align_motifs \<pwm_leader\> \<pwm_2\> \<pwm_3\> ...
-  
-  Also you can use -h option to print help for a tool in console.
-  There are lots of different command line options. Most useful option is -d <discretization=1|10|100|1000>. You can vary precision/speed rate by specifing a discretization. For more information look through a manual.
-  Some of tools also can process PCMs in addition to PWMs.
-
-## Basic usage in your code
-    require 'macroape'
-    background = [1,1,1,1]
-    discretization = 10
-    pwm_first = Bioinform::PWM.new(File.read('first_pwm.pat')).background(background).discrete(discretization)
-    pwm_second = Bioinform::PWM.new(File.read('first_pwm.pat')).background(background).discrete(discretization)
-    
-    cmp = Macroape::PWMCompare.new(pwm_first, pwm_second)
-    first_threshold = pwm_first.threshold(pvalue)
-    second_threshold = pwm_second.threshold(pvalue)
-    
-    similarity_info = cmp.jaccard(first_threshold, second_threshold)
-    puts "Jaccard similarity: #{similarity_info[:similarity]}"
-    
-  For more details look a source code of utilities in lib/macroape/cli/ folder
-
-## Contributing
-
-1. Fork it
-2. Create your feature branch (`git checkout -b my-new-feature`)
-3. Commit your changes (`git commit -am 'Added some feature'`)
-4. Push to the branch (`git push origin my-new-feature`)
-5. Create new Pull Request
-
+# Macroape
+
+Macroape is abbreviation for MAtrix CompaRisOn by Approximate P-value Estimation. It's a bioinformatic tool for evaluating similarity measure between a pair of Position Weight Matrices. Used approach and application described in manual at https://docs.google.com/document/pub?id=1_jsxhMNzMzy4d2d_byAd3n6Szg5gEcqG_Sf7w9tEqWw
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'macroape'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install macroape
+
+## Usage
+  For more information read manual at https://docs.google.com/document/pub?id=1_jsxhMNzMzy4d2d_byAd3n6Szg5gEcqG_Sf7w9tEqWw (not last version but comprehensive description of approach)
+
+## Basic usage as a command-line tool
+  MacroAPE have 7 command line tools:
+  
+### Tools for calculating thresholds and pvalues:
+  * find_threshold \<PWM file\> [-p \<pvalue\> (by default: 0.0005)]
+  * find_pvalue \<PWM file\> \<threshold\>
+  
+### Tools for evaluating Jaccard similarity measure in the best alignment and in certain alignment:
+  * eval_similarity \<first PWM file\> \<second PWM file\>
+  * eval_alignment \<first PWM file\> \<second PWM file\> \<shift of second matrix\> \<orientation of second matrix(direct|revcomp)\>
+  
+### Tools for looking through collection for the motifs most similar to a query motif
+  * preprocess_collection \<folder with motif files\> [-o \<collection output file\>]
+  * scan_collection \<query PWM file\> \<collection file\>
+  
+### Tool for finding mutual alignment of several motifs relative to first(leader) motif. It's designed to use with sequence_logo to draw logos of clusters
+  * align_motifs \<pwm_leader\> \<pwm_2\> \<pwm_3\> ...
+  
+  Also you can use -h option to print help for a tool in console.
+  There are lots of different command line options. Most useful option is -d <discretization=1|10|100|1000>. You can vary precision/speed rate by specifing a discretization. For more information look through a manual.
+  Some of tools also can process PCMs in addition to PWMs.
+
+## Basic usage in your code
+    require 'macroape'
+    background = [1,1,1,1]
+    discretization = 10
+    pwm_first = Bioinform::PWM.new(File.read('first_pwm.pat')).background(background).discrete(discretization)
+    pwm_second = Bioinform::PWM.new(File.read('first_pwm.pat')).background(background).discrete(discretization)
+    
+    cmp = Macroape::PWMCompare.new(pwm_first, pwm_second)
+    first_threshold = pwm_first.threshold(pvalue)
+    second_threshold = pwm_second.threshold(pvalue)
+    
+    similarity_info = cmp.jaccard(first_threshold, second_threshold)
+    puts "Jaccard similarity: #{similarity_info[:similarity]}"
+    
+  For more details look a source code of utilities in lib/macroape/cli/ folder
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Added some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request
+
+If you're developing both macroape and bioinform - it may be useful to know that test_helper and spec_helper expands require path in such a way that if you have two "cousin" folders: macroape and bioinform then macroape specs will require bioinform from development folder not from gem. It can save you lots of time not to rebuild-reinstall bioinform gem each time it get some changes
+
 Copyright (c) 2011-2012 Ilya Vorontsov, Ivan Kulakovskiy, Vsevolod Makeev

data/TODO.txt

@@ -10,7 +10,7 @@ Ideas to increase perfomance:
   - Possibly algorithm shouldn't use hash but had two iterations: at first it determines possible hash scores for every length(if worst suffix is always zero, its flat space of scores at all pwm prefix lengths) of each pwm separately. And after that we can work with arrays which use such scores as indices via additional substructure
   
 Usability issues:  
-  review Collection class. Now its completely unuseful. May be it should be even in another gem (with blackjack and clustering)
+  make preprocess_collection be able to add information to existing collection of motifs. Make able to give collection a name from command line
 
 remove .stdin placeholder. Use tty? method instead
 

data/benchmark/benchmark_helper.rb

@@ -0,0 +1,5 @@
+$bioinform_folder = File.expand_path(File.join(File.dirname(__FILE__), '..', '..', 'bioinform', 'lib'))
+$LOAD_PATH.unshift $bioinform_folder
+
+require 'benchmark'
+require_relative '../lib/macroape'

data/benchmark/similarity_benchmark.rb

@@ -1,7 +1,4 @@
-require 'benchmark'
-
-$:.unshift File.join(File.dirname(__FILE__),'../lib')
-require 'macroape'
+require_relative 'benchmark_helper'
 
 class TaskToBenchmark
   def setup

data/bin/align_motifs

@@ -1,4 +1,4 @@
 #!/usr/bin/env ruby
 
-require 'macroape/cli/align_motifs'
+require_relative '../lib/macroape/cli/align_motifs'
 Macroape::CLI::AlignMotifs.main(ARGV)

data/bin/eval_alignment

@@ -1,4 +1,4 @@
 #!/usr/bin/env ruby
 
-require 'macroape/cli/eval_alignment'
+require_relative '../lib/macroape/cli/eval_alignment'
 Macroape::CLI::EvalAlignment.main(ARGV)

data/bin/eval_similarity

@@ -1,4 +1,4 @@
 #!/usr/bin/env ruby
 
-require 'macroape/cli/eval_similarity'
+require_relative '../lib/macroape/cli/eval_similarity'
 Macroape::CLI::EvalSimilarity.main(ARGV)

data/bin/find_pvalue

@@ -1,4 +1,4 @@
 #!/usr/bin/env ruby
 
-require 'macroape/cli/find_pvalue'
+require_relative '../lib/macroape/cli/find_pvalue'
 Macroape::CLI::FindPValue.main(ARGV)

data/bin/find_threshold

@@ -1,4 +1,4 @@
 #!/usr/bin/env ruby
 
-require 'macroape/cli/find_threshold'
+require_relative '../lib/macroape/cli/find_threshold'
 Macroape::CLI::FindThreshold.main(ARGV)

data/bin/preprocess_collection

@@ -1,4 +1,4 @@
 #!/usr/bin/env ruby
 
-require 'macroape/cli/preprocess_collection'
+require_relative '../lib/macroape/cli/preprocess_collection'
 Macroape::CLI::PreprocessCollection.main(ARGV)

data/bin/scan_collection

@@ -1,4 +1,4 @@
 #!/usr/bin/env ruby
 
-require 'macroape/cli/scan_collection'
+require_relative '../lib/macroape/cli/scan_collection'
 Macroape::CLI::ScanCollection.main(ARGV)

data/lib/macroape/aligned_pair_intersection.rb

@@ -30,7 +30,7 @@ module Macroape
                           threshold_first - first.best_suffix(column + 1),
                           threshold_second - second.best_suffix(column + 1), &count_contribution_block)
         scores.replace(new_scores)
-        if max_hash_size && scores.inject(0){|sum,hsh|sum + hsh.size} > max_hash_size
+        if max_pair_hash_size && scores.inject(0){|sum,hsh|sum + hsh.size} > max_pair_hash_size
           raise 'Hash overflow in Macroape::AlignedPairIntersection#counts_for_two_matrices_with_different_probabilities'
         end
       end

data/lib/macroape/cli/align_motifs.rb

@@ -1,4 +1,4 @@
-require 'macroape'
+require_relative '../../macroape'
 
 module Macroape
   module CLI
@@ -15,7 +15,7 @@ module Macroape
           pwm_3_file  shift_3  orientation_3
         }
 
-        if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
+        if ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
           STDERR.puts help_string
           exit
         end
@@ -28,9 +28,9 @@ module Macroape
         pvalue = 0.0005
         
         shifts = {leader => [0,:direct]}
-        pwm_first = data_model.new(File.read(leader)).to_pwm.background!(background).discrete!(discretization)
+        pwm_first = data_model.new(File.read(leader)).to_pwm.set_parameters(background: background).discrete!(discretization)
         argv.each do |motif_name|
-          pwm_second = data_model.new(File.read(motif_name)).to_pwm.background!(background).discrete!(discretization)
+          pwm_second = data_model.new(File.read(motif_name)).to_pwm.set_parameters(background: background).discrete!(discretization)
           cmp = Macroape::PWMCompare.new(pwm_first, pwm_second)
           info = cmp.jaccard_by_pvalue(pvalue)
           shifts[motif_name] = [info[:shift], info[:orientation]]

data/lib/macroape/cli/eval_alignment.rb

@@ -1,4 +1,4 @@
-require 'macroape'
+require_relative '../../macroape'
 
 module Macroape
   module CLI
@@ -32,7 +32,7 @@ module Macroape
           cat motifs/KLF4.pat motifs/SP1.pat | ruby eval_alignment.rb .stdin .stdin 3 direct -p 0.0005 -d 100 -b 0.4 0.3 0.2 0.1
         }
 
-        if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
+        if ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
           STDERR.puts help_string
           exit
         end
@@ -91,7 +91,10 @@ module Macroape
         raise 'background should be symmetric: p(A)=p(T) and p(G) = p(C)' unless first_background == first_background.reverse
         raise 'background should be symmetric: p(A)=p(T) and p(G) = p(C)' unless second_background == second_background.reverse
 
-        parser = Bioinform::StringParser.new($stdin.read)  if first_file == '.stdin' || second_file == '.stdin'
+        if first_file == '.stdin' || second_file == '.stdin'
+          input = $stdin.read
+          parser = data_model.choose_parser(input).new(input)
+        end
       
         if first_file == '.stdin'
           input_first = parser.parse
@@ -109,10 +112,10 @@ module Macroape
         end
         pwm_second = data_model.new(input_second).to_pwm
         
-        pwm_first.background!(first_background).max_hash_size!(max_hash_size).discrete!(discretization)
-        pwm_second.background!(second_background).max_hash_size!(max_hash_size).discrete!(discretization)
+        pwm_first.set_parameters(background: first_background, max_hash_size: max_hash_size).discrete!(discretization)
+        pwm_second.set_parameters(background: second_background, max_hash_size: max_hash_size).discrete!(discretization)
 
-        cmp = Macroape::PWMCompareAligned.new(pwm_first, pwm_second, shift, orientation).max_hash_size(max_pair_hash_size)
+        cmp = Macroape::PWMCompareAligned.new(pwm_first, pwm_second, shift, orientation).set_parameters(max_pair_hash_size: max_pair_hash_size)
 
         info = cmp.alignment_infos.merge( cmp.jaccard_by_pvalue(pvalue) )
 

data/lib/macroape/cli/eval_similarity.rb

@@ -1,4 +1,4 @@
-require 'macroape'
+require_relative '../../macroape'
 
 module Macroape
   module CLI
@@ -33,7 +33,7 @@ module Macroape
           cat motifs/KLF4.pat motifs/SP1.pat | ruby eval_similarity.rb .stdin .stdin -p 0.0005 -d 100 -b 0.4 0.3 0.2 0.1
         }
 
-        if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
+        if ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
           STDERR.puts help_string
           exit
         end
@@ -73,7 +73,10 @@ module Macroape
         raise 'background should be symmetric: p(A)=p(T) and p(G) = p(C)' unless first_background == first_background.reverse
         raise 'background should be symmetric: p(A)=p(T) and p(G) = p(C)' unless second_background == second_background.reverse
 
-        parser = Bioinform::StringParser.new($stdin.read)  if first_file == '.stdin' || second_file == '.stdin'
+        if first_file == '.stdin' || second_file == '.stdin'
+          input = $stdin.read
+          parser = data_model.choose_parser(input).new(input)
+        end
         
         if first_file == '.stdin'
           input_first = parser.parse
@@ -91,10 +94,10 @@ module Macroape
         end
         pwm_second = data_model.new(input_second).to_pwm
         
-        pwm_first.background!(first_background).max_hash_size!(max_hash_size).discrete!(discretization)
-        pwm_second.background!(second_background).max_hash_size!(max_hash_size).discrete!(discretization)
+        pwm_first.set_parameters(background: first_background, max_hash_size: max_hash_size).discrete!(discretization)
+        pwm_second.set_parameters(background: second_background, max_hash_size: max_hash_size).discrete!(discretization)
 
-        cmp = Macroape::PWMCompare.new(pwm_first, pwm_second).max_hash_size(max_pair_hash_size)
+        cmp = Macroape::PWMCompare.new(pwm_first, pwm_second).set_parameters(max_pair_hash_size: max_pair_hash_size)
 
         info = cmp.jaccard_by_pvalue(pvalue)
 

data/lib/macroape/cli/find_pvalue.rb

@@ -1,4 +1,4 @@
-require 'macroape'
+require_relative '../../macroape'
 
 module Macroape
   module CLI
@@ -31,7 +31,7 @@ module Macroape
             cat motifs/KLF4.pat | ruby find_pvalue.rb .stdin 7.32 4.31 5.42
         }
       
-        if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
+        if ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
           STDERR.puts help_string
           exit
         end
@@ -75,7 +75,7 @@ module Macroape
           input = File.read(filename)
         end
         pwm = data_model.new(input).to_pwm
-        pwm.background!(background).max_hash_size!(max_hash_size).discrete!(discretization)
+        pwm.set_parameters(background: background, max_hash_size: max_hash_size).discrete!(discretization)
 
         counts = pwm.counts_by_thresholds(* thresholds.map{|count| count * discretization})
         pvalues = counts.map{|count| count.to_f / pwm.vocabulary_volume}

data/lib/macroape/cli/find_threshold.rb

@@ -1,4 +1,4 @@
-require 'macroape'
+require_relative '../../macroape'
 
 module Macroape
   module CLI
@@ -27,7 +27,7 @@ module Macroape
             ruby find_threshold.rb motifs/KLF4.pat -p 0.001 0.0001 0.0005 -d 1000 -b 0.4 0.3 0.2 0.1
         }
       
-        if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
+        if ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
           STDERR.puts help_string
           exit
         end
@@ -70,7 +70,7 @@ module Macroape
           input = File.read(filename)
         end
         pwm = data_model.new(input).to_pwm
-        pwm.background!(background).max_hash_size!(max_hash_size).discrete!(discretization)
+        pwm.set_parameters(background: background, max_hash_size: max_hash_size).discrete!(discretization)
 
         pwm.thresholds(*pvalues) do |pvalue, threshold, real_pvalue|
           puts "#{pvalue}\t#{threshold / discretization}\t#{real_pvalue}"

data/lib/macroape/cli/preprocess_collection.rb

@@ -1,5 +1,6 @@
-require 'macroape'
+require_relative '../../macroape'
 require 'yaml'
+require 'shellwords'
 
 module Macroape
   module CLI
@@ -8,13 +9,14 @@ module Macroape
       def self.main(argv)
         help_string = %q{
         Command-line format:
-          ruby preprocess_collection.rb <file or folder with PWMs or .stdin with PWMs> [options]
+          ruby preprocess_collection.rb <file or folder with PWMs or .stdin with filenames> [options]
 
         Options:
           [-p <list of P-values>]
           [-d <rough discretization> <precise discretization>]
           [-b <background probabilities, ACGT - 4 numbers, space-delimited, sum should be equal to 1>]
           [-o <output file>]
+          [-n <name>] - specify name for a collection. Default filename is based on this parameter
           [--silent] - don't show current progress information during scan (by default this information's written into stderr)
           [--pcm] - treats your input motifs as PCM-s. Motifs are converted to PWMs internally so output is the same as for according PWMs
 
@@ -24,7 +26,7 @@ module Macroape
           ruby preprocess_collection.rb ./motifs -p 0.001 0.0005 0.0001 -d 1 10 -b 0.2 0.3 0.2 0.3 -o collection.yaml
         }
 
-        if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
+        if ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
           STDERR.puts help_string
           exit
         end
@@ -35,7 +37,7 @@ module Macroape
         background = [1,1,1,1]
         rough_discretization = 1
         precise_discretization = 10
-        output_file =  'collection.yaml'
+        output_file = 'collection.yaml'
         max_hash_size = 1000000
         
         data_source = argv.shift
@@ -45,6 +47,7 @@ module Macroape
 
         pvalues = []
         silent = false
+        output_file_specified = false
         until argv.empty?
           case argv.shift
             when '-b'
@@ -63,8 +66,11 @@ module Macroape
               rough_discretization, precise_discretization = argv.shift(2).map(&:to_f).sort
             when '-o'
               output_file = argv.shift
+              output_file_specified = true
             when '-m'
               max_hash_size = argv.shift.to_i
+            when '-n'
+              collection_name = argv.shift
             when '--silent'
               silent = true
             end
@@ -75,6 +81,10 @@ module Macroape
                                 precise_discretization: precise_discretization,
                                 background: background,
                                 pvalues: pvalues)
+        if collection_name
+          collection.name = collection_name
+          output_file = "#{collection_name}.yaml"  if !output_file_specified
+        end
         
         if File.directory?(data_source)
           motifs = Dir.glob(File.join(data_source,'*')).sort.map do |filename|
@@ -84,10 +94,15 @@ module Macroape
           end
         elsif File.file?(data_source)
           input = File.read(data_source)
-          motifs = data_model.choose_parser(input).split_on_motifs(input, data_model)
+          motifs = data_model.split_on_motifs(input)
         elsif data_source == '.stdin'
-          input = $stdin.read
-          motifs = data_model.choose_parser(input).split_on_motifs(input, data_model)
+          filelist = $stdin.read.shellsplit
+          motifs = []
+          filelist.each do |filename|
+            motif = data_model.new(File.read(filename))
+            motif.name ||= File.basename(filename, File.extname(filename))
+            motifs << motif
+          end
         else
           raise "Specified data source `#{data_source}` is neither directory nor file nor even .stdin"
         end
@@ -102,19 +117,28 @@ module Macroape
           # Also two command line options to fail on skipping or to skip silently should be included
 
           info = OpenStruct.new(rough: {}, precise: {})
-          pwm.background!(background).max_hash_size!(max_hash_size)
+          pwm.set_parameters(background: background, max_hash_size: max_hash_size)
+          skip_motif = false
 
           pwm.discrete(rough_discretization).thresholds(*pvalues) do |pvalue, threshold, real_pvalue|
-            info.rough[pvalue] = threshold / rough_discretization
+            if real_pvalue == 0
+              $stderr.puts "#{pwm.name} at pvalue #{pvalue} has threshold that yields real-pvalue 0 in rough mode. Rough calculation will be skipped"
+            else
+              info.rough[pvalue] = threshold / rough_discretization
+            end
           end
 
           pwm.discrete(precise_discretization).thresholds(*pvalues) do |pvalue, threshold, real_pvalue|
-            info.precise[pvalue] = threshold / precise_discretization
+            if real_pvalue == 0
+              $stderr.puts "#{pwm.name} at pvalue #{pvalue} has threshold that yields real-pvalue 0 in precise mode. Motif will be excluded from collection"
+              skip_motif = true
+            else
+              info.precise[pvalue] = threshold / precise_discretization
+            end
           end
-
-          collection.add_pm(pwm, info)
+          collection.add_pm(pwm, info)  unless skip_motif
         end
-        File.open(output_file,'w') do |f|
+        File.open(output_file, 'w') do |f|
           f.puts(collection.to_yaml)
         end
       rescue => err