semtools 0.1.6 → 0.1.9

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: semtools
 version: !ruby/object:Gem::Version
-  version: 0.1.6
+  version: 0.1.9
 platform: ruby
 authors:
 - seoanezonjic
@@ -9,7 +9,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-05-27 00:00:00.000000000 Z
+date: 2025-09-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: text
@@ -25,6 +25,34 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: down
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: expcalc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
@@ -75,6 +103,7 @@ email:
 executables:
 - console
 - onto2json.rb
+- semtools.rb
 - setup
 - strsimnet.rb
 extensions: []
@@ -90,13 +119,17 @@ files:
 - Rakefile
 - bin/console
 - bin/onto2json.rb
+- bin/semtools.rb
 - bin/setup
 - bin/strsimnet.rb
+- external_data/ontologies.txt
 - lib/data/hp.obo
 - lib/data/phenotype_annotation.tab
 - lib/semtools.rb
-- lib/semtools/math_methods.rb
 - lib/semtools/ontology.rb
+- lib/semtools/parsers/file_parser.rb
+- lib/semtools/parsers/json_parser.rb
+- lib/semtools/parsers/oboparser.rb
 - lib/semtools/sim_handler.rb
 - lib/semtools/version.rb
 - semtools.gemspec
@@ -119,9 +152,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.3
+rubygems_version: 3.3.7
 signing_key:
 specification_version: 4
-summary: Gem to handle semantic based calculations in text and defined ontologies
-  as GO or HPO.
+summary: 'DEPRECATED PROJECT. MIGRATED TO PYTHON: https://github.com/seoanezonjic/py_semtools.
+  Gem to handle semantic based calculations in text and defined ontologies as GO or
+  HPO.'
 test_files: []

data/lib/semtools/math_methods.rb

@@ -1,148 +0,0 @@
-# TODO: Make a pull request to https://rubygems.org/gems/ruby-statistics, with all the statistic code implemented here.
-#to cmpute fisher exact test
-#Fisher => http://www.biostathandbook.com/fishers.html
-def get_fisher_exact_test(listA, listB, all_elements_count, tail ='two_sided', weigths=nil, partial_weigths=true)
-	#puts '-', listA.inspect, listB.inspect, '-'
-	listA_listB = listA & listB
-	listA_nolistB = listA - listB
-	nolistA_listB = listB - listA
-	if weigths.nil?
-		listA_listB_count = listA_listB.length
-		listA_nolistB_count = listA_nolistB.length
-		nolistA_listB_count = nolistA_listB.length
-		nolistA_nolistB_count = all_elements_count - (listA | listB).length
-	else
-		# Fisher exact test weigthed as proposed in Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
-		# https://academic.oup.com/bioinformatics/article/22/13/1600/193669
-		listA_listB_count = listA_listB.map{|i| weigths[i]}.inject(0){|sum, n| sum + n}.ceil
-		listA_nolistB_count = listA_nolistB.map{|i| weigths[i]}.inject(0){|sum, n| sum + n}.ceil
-		nolistA_listB_count = nolistA_listB.map{|i| weigths[i]}.inject(0){|sum, n| sum + n}.ceil
-
-		if partial_weigths
-			nolistA_nolistB_count = all_elements_count - (listA | listB).length
-			all_elements_count = nolistA_nolistB_count + listA_listB_count + listA_nolistB_count + nolistA_listB_count
-		else
-			nolistA_nolistB_count = (weigths.keys - (listA | listB)).map{|i| weigths[i]}.inject(0){|sum, n| sum + n}.ceil
-			all_elements_count = weigths.values.inject(0){|sum, n| sum + n}.ceil
-		end
-	end
-	#puts [listA_listB_count, listA_nolistB_count, nolistA_listB_count, nolistA_nolistB_count, all_elements_count].inspect
-	if tail == 'two_sided'
-		accumulated_prob = get_two_tail(listA_listB_count, listA_nolistB_count, nolistA_listB_count, nolistA_nolistB_count, all_elements_count)
-	elsif tail == 'less' 
-		accumulated_prob = get_less_tail(listA_listB_count, listA_nolistB_count, nolistA_listB_count, nolistA_nolistB_count, all_elements_count)
-	end
-	return accumulated_prob
-end
-
-def get_two_tail(listA_listB_count, listA_nolistB_count, nolistA_listB_count, nolistA_nolistB_count, all_elements_count)
-	#https://www.sheffield.ac.uk/polopoly_fs/1.43998!/file/tutorial-9-fishers.pdf
-	accumulated_prob = 0
-	ref_prob = compute_hyper_prob(
-		listA_listB_count, 
-		listA_nolistB_count, 
-		nolistA_listB_count, 
-		nolistA_nolistB_count, 
-		all_elements_count
-	)
-	accumulated_prob += ref_prob
-	[listA_listB_count, nolistA_nolistB_count].min.times do |n| #less
-		n += 1
-		prob = compute_hyper_prob(
-			listA_listB_count - n, 
-			listA_nolistB_count + n, 
-			nolistA_listB_count + n, 
-			nolistA_nolistB_count - n, 
-			all_elements_count
-		)
-		prob <= ref_prob ? accumulated_prob += prob : break
-	end
-
-	[listA_nolistB_count, nolistA_listB_count].min.times do |n| #greater
-		n += 1
-		prob = compute_hyper_prob(
-			listA_listB_count + n, 
-			listA_nolistB_count - n, 
-			nolistA_listB_count - n, 
-			nolistA_nolistB_count + n, 
-			all_elements_count
-		)
-		accumulated_prob += prob if prob <= ref_prob
-	end
-
-	return accumulated_prob
-end
-
-def get_less_tail(listA_listB_count, listA_nolistB_count, nolistA_listB_count, nolistA_nolistB_count, all_elements_count)
-	accumulated_prob = 0
-	[listA_listB_count, nolistA_nolistB_count].min.times do |n|
-		accumulated_prob += compute_hyper_prob(
-			listA_listB_count - n, 
-			listA_nolistB_count + n, 
-			nolistA_listB_count + n, 
-			nolistA_nolistB_count - n, 
-			all_elements_count
-		)
-	end
-	return accumulated_prob
-end
-
-def compute_hyper_prob(a, b, c, d, n)
-	# https://en.wikipedia.org/wiki/Fisher%27s_exact_test
-	binomA = binom(a + b, a)
-	binomC = binom(c + d, c)
-	divisor = binom(n, a + c)
-	return (binomA * binomC).fdiv(divisor)
-end
-
-def binom(n,k)
-	if k > 0 && k < n
-		res = (1+n-k..n).inject(:*)/(1..k).inject(:*)
-	else
-		res = 1
-	end
-end
-
-#to cmpute adjusted pvalues
-#https://rosettacode.org/wiki/P-value_correction#Ruby
-def get_benjaminiHochberg_pvalues(arr_pvalues)
-	n = arr_pvalues.length
-	arr_o = order(arr_pvalues, true)
-	arr_cummin_input = []
-	(0..(n - 1)).each do |i|
-		arr_cummin_input[i] = (n / (n - i).to_f) * arr_pvalues[arr_o[i]]
-	end
-	arr_ro = order(arr_o)
-	arr_cummin = cummin(arr_cummin_input)
-	arr_pmin = pmin(arr_cummin)
-	return arr_pmin.values_at(*arr_ro)
-end
-
-def order(array, decreasing = false)
-	if decreasing == false
-		array.sort.map { |n| array.index(n) }
-	else
-		array.sort.map { |n| array.index(n) }.reverse
-	end
-end
-
-def cummin(array)
-	cumulative_min = array.first
-	arr_cummin = []
-	array.each do |p|
-		cumulative_min = [p, cumulative_min].min
-		arr_cummin << cumulative_min
-	end
-	return arr_cummin
-end
-
-def pmin(array)
-	x = 1
-	pmin_array = []
-	array.each_index do |i|
-		pmin_array[i] = [array[i], x].min
-		abort if pmin_array[i] > 1
-	end
-	return pmin_array
-end
-