melt_baseline 0.1.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA256:
+  metadata.gz: 13b370dda90d4cf095f6c37ce88568e1c9df683504eea5324a5309e62a559cfa
+  data.tar.gz: 3ef3964e6f6fab2729f1b7525e6bed72f4340fbddc2bfbb157732c73b6262053
+SHA512:
+  metadata.gz: 871bfb732c0d287b16a1e415c702bedc49dfca3ad44beff84485e9a68dc5ecb0b45c77fc1945c8262fa22368cfe72c1bd0f0d079b0b95e24536248666ab2f837
+  data.tar.gz: 455e1197b4b1b0be95d1df12b428b9a43b550a51f4a972f73d4176b404bc50c6ac6094a760034602498cb4270c176716e9301ae6c1ce2bfb314563df25eb7d6a

data/lib/melt_baseline.rb

@@ -0,0 +1,113 @@
+#  High-Resolution Melting Background Removal (MeltBaseline)
+
+##############################################################
+# MIT License
+
+# Copyright (c) [2020] [ZACHARY L. DWIGHT]
+
+# 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.
+##############################################################
+
+# Important Note: MELTING CURVE ANALYSIS Data Generation IP
+
+# The generation of actual melt data may be covered by 
+# U.S. Patent Nos. 7,582,429; 7,803,551; 8,068,992; 8,093,002; 
+# 8,296,074; 9,273,346; and other U.S. and foreign patents and 
+# patent applications owned by the University of Utah Research 
+# Foundation and licensed to BioFire Defense, LLC. 
+
+# If your PCR instrument is not licensed under these patents, 
+# please contact Jill Powlick at bioMerieux (jill.powlick@biomerieux.com) 
+# for sublicensing information.
+
+
+
+#INPUTS DEFINED
+
+#t is the array of temperatures
+#h is the array of raw fluorescence values
+#c is the width of the cursors (areas before and after melt occurs)
+
+#OUTPUT DEFINED
+# returns new array of fluorescence values, user may want to normalize to 100%
+# as opposed to 1 (max helicity) and 0 (no helicity)
+
+module MELTBASELINE
+class MeltCurve
+  def self.normalize(hs,ts,cw)
+    # Select a number of points that represents the region BEFORE melting
+    tcstart = 0
+    tcend = cw
+    
+    # Select a number of points that represents the region AFTER melting
+    bcstart = hs.length() - cw
+    bcend = hs.length() - 1
+    
+    #find slope of cursor regions
+    m1 = self.getslope(ts[tcstart],ts[tcend],hs[tcstart],hs[tcend])
+    m2 = self.getslope(ts[bcstart],ts[bcend],hs[bcstart],hs[bcend])
+    
+    #define intercepts
+    b1 = self.getintercept(ts[tcend],hs[tcend],m1)
+    b2 = self.getintercept(ts[bcstart],hs[bcstart],m2)
+    newF = 1.000
+    a = []
+    for i in (0..hs.length()-1)
+		topF=self.getpoint(m1,ts[i],b1);
+		
+		botF=self.getpoint(m2,ts[i],b2);
+		
+		newF = (hs[i].to_f - botF.to_f )/(topF.to_f - botF.to_f );
+		if(newF < 0 )
+			newF = 0
+		end
+		if(newF > 1)
+			newF = 1
+		end
+		a.push(newF);	
+	end
+    return a
+  end
+  
+  def self.getintercept(x,y,m)
+	b = y-(x*m)
+	return b
+  end
+  
+  def self.getpoint(m,x,b)
+	point = m*x+b
+	return point
+  end
+  
+  def self.getslope(t1,t2,f1,f2)
+	slope = (f2-f1)/(t2-t1)
+	return slope
+  end
+
+end
+end
+
+##### EXAMPLE USAGE #####
+# require 'melt_baseline'
+
+# t = [60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95]
+# h = [61572,60624,59537,58351,56644,54569,53361,51715,49491,48180,46515,45691,45097,44579,44050,44440,43907,39960,33507,26271,18696,11805,6121,2377,1278,2492,3287,3259,3184,3180,3094,2993,2880,2683,2508,2342]
+# c = 6
+
+# puts MELTBASELINE::MeltCurve.normalize(h,t,c)

metadata

@@ -0,0 +1,47 @@
+--- !ruby/object:Gem::Specification
+name: melt_baseline
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Zachary L. Dwight
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2020-10-27 00:00:00.000000000 Z
+dependencies: []
+description: 'A Ruby gem used for High-Resolution Melting (HRM) background signal
+  removal using a baseline method similar to that described by Wittwer & Palais (2009).  DOI:
+  10.1016/S0076-6879(08)03813-5.'
+email: zach.dwight@path.utah.edu
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- lib/melt_baseline.rb
+homepage: https://dna-utah.org
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.7.6
+signing_key: 
+specification_version: 4
+summary: High-Resolution DNA Melting Curve Background Removal Baseline Method (Molecular
+  Diagnostics)
+test_files: []