quorum 0.3.2 → 0.3.3

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    quorum (0.3.2)
+    quorum (0.3.3)
       bio-blastxmlparser (~> 1.0.1)
       jquery-rails
       net-ssh (~> 2.3.0)
@@ -54,7 +54,7 @@ GEM
       rack-test (>= 0.5.4)
       selenium-webdriver (~> 2.0)
       xpath (~> 0.1.4)
-    childprocess (0.3.2)
+    childprocess (0.3.3)
       ffi (~> 1.0.6)
     database_cleaner (0.8.0)
     diff-lcs (1.1.3)
@@ -78,7 +78,7 @@ GEM
       railties (>= 3.2.0, < 5.0)
       thor (~> 0.14)
     json (1.7.3)
-    libwebsocket (0.1.3)
+    libwebsocket (0.1.4)
       addressable
     log4r (1.1.10)
     mail (2.4.4)
@@ -89,7 +89,7 @@ GEM
     multi_json (1.3.6)
     mysql2 (0.3.11)
     net-ssh (2.3.0)
-    nokogiri (1.5.4)
+    nokogiri (1.5.5)
     polyglot (0.3.3)
     rack (1.4.1)
     rack-cache (1.2)
@@ -134,21 +134,21 @@ GEM
     resque_spec (0.12.2)
       resque (>= 1.19.0)
       rspec (>= 2.5.0)
-    rspec (2.10.0)
-      rspec-core (~> 2.10.0)
-      rspec-expectations (~> 2.10.0)
-      rspec-mocks (~> 2.10.0)
-    rspec-core (2.10.1)
-    rspec-expectations (2.10.0)
+    rspec (2.11.0)
+      rspec-core (~> 2.11.0)
+      rspec-expectations (~> 2.11.0)
+      rspec-mocks (~> 2.11.0)
+    rspec-core (2.11.1)
+    rspec-expectations (2.11.1)
       diff-lcs (~> 1.1.3)
-    rspec-mocks (2.10.1)
-    rspec-rails (2.10.1)
+    rspec-mocks (2.11.1)
+    rspec-rails (2.11.0)
       actionpack (>= 3.0)
       activesupport (>= 3.0)
       railties (>= 3.0)
-      rspec (~> 2.10.0)
+      rspec (~> 2.11.0)
     rubyzip (0.9.9)
-    selenium-webdriver (2.24.0)
+    selenium-webdriver (2.25.0)
       childprocess (>= 0.2.5)
       libwebsocket (~> 0.1.3)
       multi_json (~> 1.0)
@@ -161,7 +161,7 @@ GEM
       hike (~> 1.2)
       rack (~> 1.0)
       tilt (~> 1.1, != 1.3.0)
-    thor (0.15.3)
+    thor (0.15.4)
     tilt (1.3.3)
     treetop (1.4.10)
       polyglot

data/HISTORY.md

@@ -1,4 +1,9 @@
-## 0.3.2 (2012-06--22)
+## 0.3.3 (2012-07-19)
+
+* Fixed discover input sequence type bug. Upper and lowercase
+  input sequences are typed correctly.
+
+## 0.3.2 (2012-06-22)
 
 * Added support for user defined callback in QUORUM.pollResults().
   Useful if user chooses to define their own view template(s).

data/lib/quorum/sequence.rb

@@ -58,25 +58,26 @@ module Quorum
       # Remove the sequence FASTA header.
       seq = sequence.slice(start..-1).gsub!(/\n/, '')
 
-      if seq =~ /[EQILFP]+/
+      if seq =~ /[EQILFPeqilfp]+/
         type = "amino_acid"
       else
         # Length of the sequence minus the FASTA header.
         len = seq.length.to_f
 
         na_percent = 15.0
+        counts     = []
 
-        a = (seq.count("A").to_f / len) * 100
-        t = (seq.count("T").to_f / len) * 100
-        u = (seq.count("U").to_f / len) * 100
+        counts << (seq.count("Aa").to_f / len) * 100
+        counts << (seq.count("Tt").to_f / len) * 100
+        counts << (seq.count("Uu").to_f / len) * 100
 
-        g = (seq.count("G").to_f / len) * 100
-        c = (seq.count("C").to_f / len) * 100
+        counts << (seq.count("Gg").to_f / len) * 100
+        counts << (seq.count("Cc").to_f / len) * 100
 
-        n = (seq.count("N").to_f / len) * 100
+        counts << (seq.count("Nn").to_f / len) * 100
 
-        if (a >= na_percent) || (t >= na_percent) || (u >= na_percent) ||
-          (g >= na_percent) || (c >= na_percent) || (n >= na_percent)
+        counts.reject! { |c| c < na_percent }
+        if (!counts.empty?)
           type = "nucleic_acid"
         else
           type = "amino_acid"

data/lib/quorum/version.rb

@@ -1,3 +1,3 @@
 module Quorum
-  VERSION = "0.3.2"
+  VERSION = "0.3.3"
 end

data/spec/data/nucl_seqs_lower.txt

@@ -0,0 +1,17 @@
+>Lowercase_sequnce
+tgataggataattctagacaaaacattagccgatcaagtgtcatcatggaaaagcagcaggggccttagtgatacagtggtgactgatcatgcttgttctggggaaacatgctcgtactacgcaattggagatgtatttatttgtgaaaagactggacaagttcatgtttgtgacgaaacatgtagggaagtagtaatggatcccaccaacgagcttttggtctgtacaatatctggccactgttttgacagattgctatcacctgctgaaatggagcctgatgctgagcagcagcaaggtggtgcggcagatgaggcagaaccgtttatgggatctggccgttttgcacgggcttatttgctgggatacaattgtgctgatgaaaaggagcttgaagctactttgaggttttgctgatccctattggcccttctggagtggatgatctcatgtctcagcatttacctatttaagatcaaataaatcgggtttccttttcgtgtttctcttggcataagaatgtttgattagatctagattatgaaactctaatcgtcttctatattaataattgtatgcttaaatttatagttgaaattccattgatgaatttttctt
+cagaagacatgtctttgacaaaggtataccatcttttccnccaacttggtttgagacatttatttgttgtacctcgtccatcgcgtgtgcttggtttgataaccagaaaagatttgttgattgaggacacagatgcgaatacattagagcttcaggcaactagtagttcggcatccaggtaaaagattgatggcaaggaatgcagatgtggagagccctctgctaaatggtcttctggttcagaatcagatacctgactaataccgtctgcagccttcccgaattcctttttgcgtcccattttcacttgaaaatcattctttattatttttgtattaatgttgaaataggttagagaacccgatattttggggatggaacggggttgtagactgacagtataccctagaattttgtatataaagtataaactacagcaagcacagaaaaaaatcatgaaagcgcccttgtgataattatgatagcagaatttagactgat
+ctctctctctctctctctctctctctctccgtcgtcgttttgggttctgcggatcggtggattctggtcgcgaattccgacgctgttcgtggcggcgaaccgaattccggtcaacaagcgaagaagatgaaggttttcgtcaagactctgaagggctctcacttcgaaatcgaagtcaagccccaagacacggtttcggatgtgaagaaaaatattgaaactgttcaaggtggatgtctatcctgccgcgcagcaaatgcttattcatcaagggaaagttcttaaggatggtactaccttggaggaaaataaagtagctgaaaatagtttcattgtgattatgatttccaagagtaagactccgtctggtgaaggatctactacttcagctgcaccttcagctaaggctccagctcctgctcctatatcttcgggcacggctgtggaaggttctgatgtctatggacaagcagcatccaatctggttgctggtagcaacttggaagacacaattcagcaaattcttgatgttggaggagggacctgggatagggatactgtagtccgggctcttcgagctgccttcaacaaccctgagagagctattgaatatttatattcaggaatccccgagcaagctgaagctccacctgtgggccgtgtgcctgcaagtgcacaacctgcaaatcctccagcagctgcagctccgcaagcggcacaacctgctcctgttacctcaagtgggcctaatgctaatcctttagacctttttccacagggcctcccaaatgttggttctggtggtgctggtgctggtgctggctctttagattttcttcgcaacagccaacaattccaagccttgcgagctatggtgcaggctaatccacaaatattgcagcctatgctacaagagcttggcaaacagaatcctcatctaatgagattgattcgagatcatcaagctgacttccttcgcttgataaatgagcctgtggaaggtggcgaagggaacccattggggcagctggctggtggcataccacaagcaataactgtcacccctgaggagcgccaagcaattgaacgtcttgaagcaatgggtttcgatcgtgcgattgtattggaggtgttcttcgcttgcaacaaaaatgaggaattggctgccaactaccttttagatcacatgcatgagttcgacgaacaataaatctcttcatgttgctaaattatttatctgttatctttttaatgtttatggggcctttgttttactagacggtttgatgaggtaatacttgaaaatgaaaaaaatctcaagtggagaaggaacgtttttaccacctccacattattgcctttgtggacagtctcagtattcatatacatagtcgtttgtcctgtactattggtattgtgcatccttttaacatgtgtaattgtttagctgcgcatcctattctatattttct
+cgttcgcattgttcactcaccatacgcacttccattttcatctcccaccgtcgcattttcttcggatctgaaattcctcaccatgaatcgccaccacgatcccaatccattcgacgaagacgaagtcaatcccttctcgaacggtgctgctcctggatctaaatcacgtattccaccattggcatccgaaccactgggctttggtcaaagacatgatgctacagttgatattcctttggataccacaaatgagcctaaaaaaaaaggtcaagagctagcagcttgggaagcagatttgaaaaggagagaaaaggatttaaaaagaagagaggatgctgtttctagagctggtgtgcctgttgatgataagaattggcctccgattttcccaattattcaccatgatattgccaatgagataccggttcatgctcagaggctgcaatatttggcctttgcaagttggttaggaattgttctctgccttgtttttaatgtagttgctgtgatggtctgttggatcagaggcggtggtgttaaaatttttttccttgcggtgatctatgctctacttggtgttcccctttcatatgtgctttggtacaggcccctttatcgtgctatgaggacggatagtgcactgaagtttggctggtttttcatgttctacttgcttcatattgcattttgcatctttgctgcaattgcacctccagttgtttttcatgggaaatcattaacgggcatccttgcagcaactgacgtcttctcagaccatgtattggttgggatattctatttggttggatttggcctgttttgcttggagtctcttctaagcttgtgggtaattcagaaaatatacctgtttttccgggggcataagtgaggctactcaggattttgatccatcggcttttatgatatcagtcacttcccggcgtggcttagtatattctttctttttgtctatcctcttttttcgcttgcaatattttcgtgtgatattgtttgttgttgtagtctagttcttgttacagagcttagtgtgtaatttcctgtgtaatgaattctgtgaagtttagtaattttctagtgtaacaataaccaagctttgctttcgataagcatatatgtagtggatttccataaggaattattgtagtgctattgtagttgtgaatagtgacacccctcggaggttttctatttgtaagacagcactgatgcaaacactttagttaaaattcatgtaggatctattcaatt
+caggatacacctccagatggggaaaatatgacaggagcctccaaagagatgaatgtagaatctattccttccttctttcaagatattattgagcgtatggtttcctcacaagttatgactgtgaagcctgatgcttgcattgtggatttctataatgagggcgatcactcacatccctacaattggccacattggtatggaaggcctgtctatatcctttccctgacagaatgtgatatgactttaggaagagtaatttcctcagaccatccaggggattacaggggctctctgaagctttctcttctccctgggtctcttctgtcaaggcaagggaaatctactaattttgctagatatgctattccttctatccgcaaacaacgcatacttgttatttttacaaagtcccaaccaaagaagtcactgtcaagtgatgctcaacgttttacctcatcagcagcatcttctcattggggtccaccgccaagccgttcccccaatcacgttcgtcatcatttaggccacaagcattatgcttcagctccaacaaacggaggactgccagctccaccaatccggccaca
+aaggactagttgatttgctacatgtgttctgtgttgttcttgctttggtaaatgtgtctctagtgaaagcagaagatccatacaagttctacacatggacagtgacttatggaactctttctcctctgggcagtcctcaacaagttattctgatcaatggtcagtttcctggtccaagacttgacttggtaactaatgacaacgtgattctcaacctcatcaacaagctggatgagccattcttgctcacatggaatggcattaagcagaggaaaaattcttggcaagatggggttttaggaactaactgtcccattcctccaaactcaaattacacttacaagtttcaggccaaggatcagattggcacttatacatactttccatcaactaagatgcataaagcttctggagggtttggagctctcaatgttcttcatagatctgtcatcccaatcccttatccaaaccctgatggagattttacattactcattggtgattggtacaaaactagccacaagacattaagccaaacattggattctgggaaatctcttgcctttcctgatggcctccttatcaatggccaggctcattctaccttcactgttaaccagggaaaaacctatatgttcaggatctcaaatgttggtctgtcaacctcaattaacttcagaattcagggacataccctaaaactagttgaggttgaaggatcacacactatccagaacgaatacgactcgcttgatgtgcatgttggccaatcagtttctgtgttagtaaccttaaatcaacctccaaaggactattacatcgttgcctcaacaagatttaccaagactgttctcactacaacctcagtgctacactaaaattctcagtcagccgcatcaggatccttgcctgctccccctgctgacaat
+attgaaatacgtcttgcaaaagctgaagctattaattggacatctctcgaatatagcaaggatatgcctccccaaaaaattaaagtgcctacaattcaatctgaaaggcctgcatacccatcatcaaagccaaggacaaaagattgggataagttggaagctatggtgaaaaaagaggagaaagaagaaaagctggatggtgatgctgctttgaataaattgttccgtgatatttatcaaaatgctgatgaggacatgcggagagcaatgagcaagtcatttctggagtcaaatggaacagtgctgtcaacggattggaaagaagtgggatccaagaaggtggaaggaagtcctccagaaggtatggaattgaagaaatgggagtactaattcagtacaagctgatgctcatgagagttcaaattcacaaaaataaattctgagaagggaaacaaattctgtaatcttaatggtatcggttattttg
+tgagatcatgcgcgaaatgatgaggaatacagacagagccatgagcaacattgagtcttctcctgagggattcaacatgctgaggcgcatgtatgaaaatgttcaagaaccatttttaaatgccactacaatggctggtaatacaggaaatgatggtgtcaggaatcaatcaactaatccctcaacgactaattctgaagcaacttcccctgttccaaatactaacccacttcctaatccttggtcctccactggaactggaggtgcacaaggcaacaccagaaggacaactgctggtggggatgctcggcagcaggcactcactggactaggaggacttggtgtgccagatcttgaaggcatgatgggtggtatgccagatcctgctatgttgacccaattaatgcaaaatccagctatttcacaaatgatgcagagtatcctttccaatccacagactatgaatcagattcttggtctcaatactgagcagcgtggcatgcctgatctaaactcactaagaagatgtgatgcaaaacccagagtttcttcgcttattttcctcacctgagacactgcagcaactcatgtctttccagcaatctcttatgtctcaagttgg
+cagctctattctccaccaacacaaaaacgctcacaaactagcttctttggagaaaacattagagacaatagtggcggtggtgggaacaatggcagcctcactacaagcagcagctactttcatgcaaccaaccaagtttggtcgcaccaacactttgcagctgaaatctactcaatccatttctaaggcttttgggttggagccctctgcagctaaggtctcatgttcccttcaggctgatttcaaggagttggctcacaagtgtgttgaagctaccaagattgctgggtttgctcttgccacctctgctctagttgtctctggagcaagtgcggaaggtgctccgaagaggctaaccttcgatgaaatccagagcaagacatacatggaagtgaagggaaccggaaccgcaaaccagtgccccaccattgaagggggagtggaatcattttccttcaaggccgggaagtacaatgccaagaagttctgccttgaacccacttcattcacagtgaaggcagagggagtagccaagaacgccccacttgagttccaaaacaccaagctcatgacacgtctgacctacaccctcgacgagatcgaaggaccctttgaggtttcctctgatggcactgtcaagttcgaggagaaagatggcattgactacgctgctgtcacagttcagcttcccggtggcgagcgtgttccattccttttcaccatcaaacagttggtagcatctgggaagccagacagcttcagtggggagtttctagtgccttcataccgtggatcttccttcttggaccccaagggaagaggtgcgtcaactggttatgacaatgctgtcgcattgcctgctggtggcagaggagatgaggaagaacttgctaaggagaacaaccagagtgcttcttcatcccaagggaagatcaccttgagcgtgacacagagcaagcctgataccggtgaggtgattggtgtgttcgagagcattcagccgtccgacactgatttgggagcgaaagctcccaaggatgtgaagatccagggagtttggtatgctcagctcgagtcatagacagctttatctctcttctgctttattttgtattttgttgtaacttctcagtgttgctgccattacctttgacaccactgtcccagcatgagagtgttatccttgtttgtatgtatactatcgactttcaattataatgctcgaaaatgtccaaggttt
+agcagtgttcccatgaaaccttcccactgagtcaactcactctgtacataaaaccctcttcatcatcatcatggcttctcaagtttttcttcagcaagggttgttactgtttgccccaaaccaatgttctccaaccaagctcggtgtatcttcttgcctcggttctcgtaactttccgttgatttcctccacctcaatttcatggcgttgcaacaaccctctctctgccaaaccctcttttgttgtcagagctgactccaatgtcgacgctgcttccgacaatgctggtgaagttccagaagctgaaggtagcgttgatcaggttcctgaagatggagaagcagaactagcttcggattctgaggtggagcaacccaagccccctagaaagcaacgagtcaagcttggagatgttatggggatattgaatcagagggcaattgaggcatcggaaagcatgaggccgactccagaaattaggactggagatgttgtggaaatcaaactggaagttcctgagaacaagcgtaggttgtctatttataaaggtatagtcatctcaagacaaaatgctggtattcacacaactattcgaatccgaaggattattgctggcacaggggttgagattgtcttcccaatttactcaccaaacatcaaagaaatcaaagtggtaaaccaccgtaaagtcagaagagcaagattgtactatttaagagacaagcttcccagattctccactttcaaatgatacggttaccacttctcatcctgatcttcttcaaagtagttgctgatattgcagggccatattttggttatttcgttttgttgtgttgtagaatatatcatttttcttcctctaaatctatcctccgagaattggaaacaagtgtatgtatgttgcccttgataatatttgaaatttgaagtgttctcccttgcattccttggtataggatagaaagccaagctcctaaacaaacattactaaatatgacagtctaaggaatgagcatgtgtatcgataccagttaagtgcattgtgaatgtattttttttttttatctctatccataaaaaaaggtatgttcattcttg
+aagaaacaagagagagaagatgatttagatgagccaaaaacaaaggaaaaacggcaaaagggagagaaaggaaaatctccatcaggttttcttgctcctctccagctatctgatgcccttgtaaacttccttggtactggagaaagtgaattatcaagatctgatgtcataaaaagaatgtgggaatacataaaaggaaacgaccttcaggatccttctgacaagaggaaaatattatgcgacgacaagctgaaagaactctttgatgtggactcctttaacggcttcaccgttacaaaactgttgactcctcattttataaaggcagagcagtgagttgcttgtggaaatcggtaatgttgtccaattaggtttggaaggtccttcttttgtggccttttggcattgtctgccaacacgaggaataggaattaggaacatgacagattttcagtaaatttttctccaagaatttaatgttacgtgaccattactttgttttttttaatatcacgttttgtcacttggcagttgaaatttttgtatattttcagttcctgaagctgcaaggataatgctgacttcttactctactctgcatttgctcatatgaggcactacacatatccataatacatgaataaatttgcagtattgaa
+catttgttccatttgctcaggcatttgcagctgtacttacagctgtccttactggttctctctattatgtggctgcctctcctaaagatcctacttatattgtggcacctgttttacagtctcgctctggtcgtcaagatttgaaaaagctatttgaagcctggtatgagaaacggcaaatgaaaaaaatatattcaccacttctggaaggactactagctctctacctaggatttgagtggatccaaacgaataacattcttgctcccattatcacacatggcatatactccacagttatattgggacatggcctttggaagataaacgaccaccggcgaagactacgtcaaagaatccaacagctcaaatctgaagaacaaaattcccagtagactttgaaataccttccatgtctggctgtgatacaaaaaatgtatatgtatgtattagagctgctaattatgtaaagagaaaagatgtatatacttgtgttagctgaggtctcgtacacactgaatattcaggttttgttcaccattttctaatttcgagttactatatgtagtgttttctaataaaatgaaataaaatccccaagttgggttgatttaaatt
+gagacctgttatgattcacagagccattctaggatctgttgagcgcatgtttgccattcttttagagcactacaagggtaaatggcccttgtggctcagtcctcgtcaagcaattgtatgtcctgtgtcagagaaatcacaagcttatgcactgcaggtgcgagatcagatccaccaagcaggatatcacgttgatgctgatacaactgatcggaagattcagaagaaggtacgggaagctcaattagcgcagtacaactacatcttggttgttggagaggaggaagctaatacaggacaggtgagtgtacgggttagagataaagcagaccatagcgttatgagtattgagaatctactcaaacacttcagcgacgaagttgcagcttttcattgatacttctcttgtgaaaactgttggaagcaaattttacccccactcacctagtttgttcacactttgtgtgcattatttatattttcagcctgacaatttacatttagatgatttgggtaatgactgtattttctatgtgaattttggagcgcactgatatcgatccattgtttgaaaagctgagagaaagtgtaatcttttattttctgtctacattttaattatgtttttcgttagttttttccttttatatatttgtttgttaaattgaaggaaactattgttgg
+ggcaccagggatcttacaaggctggatctccataataacaagttgacagggcctattcctcctcaaattggacggttgaagcgtcttaaaatactcaatttgaggtggaacaaactacaggatgcaattcctccagaaattggcgagcttaaaagtttaacacatctgtacctaagcttcaatagtttcaagggagaaattcccaaagagctagcaaatcttccagaccttcgctacctttatcttcatgaaaaccgtttaattggtaggataccacctgagttgggcactctacaaaaccttcggcacttggatgctggtaacaatcatttggtgggtaccataagggaactcattcgtattgaaggttgctttccagcactccgcaatctatatctaaacaataattattttactggaggaatgcctgcacaacttgccaacttatccagtcttgagatcttgtacctgtcctacaataaaatgtcaggagttataccatctagccttgctcatattcctaaattgacatacttgtacttggatcacaatcagttttcggggagaattcccgaacccttttacaaacattcatttttgaaagaaatgtacatcgagggaaatgcattccggcctggtgttaaacccattggtttccataaagtgcttgaagtttctgattcagacttccttgtttaatgaaactcaacatatttagttttttaggaagtttacgtgtataattaatgaaacaatagctcctctgattttctcaatgaaaattgctatatgggtaattcaatttttgtcacggctgtcttgtcagaagaatcaataaataatagtgttttttaactct
+ggaaatgagcacaatgttaagcagatcaagaattaccgccaaaaggttgaggaggaactctccaaaatttgtggtgacatcctgactattatagaccagcatctaattccttcttccgcctcagcagaagctagtgttttctactataagatgaaaggtgattattatcggtatcttgctgagttcaagaccgaccaagaaaggaaagaggcagccgagcagtcactcaagggatatgaggctgcttcagccactgccaacaccgatcttccatcaacacatccaatccgtcttggacttgctctcaacttctctgtcttttattacgagatcatgaactctcctgaaagggcctgccatttggctaaacaagcttttgatgaggcaattgcagagttggacaccttgagtgaagagtcatacaaggacagtactttgatcatgcagttgttgagagacaacctgactctctggacatccgatttgccagaagatggaggcgaggagaacataaaagctgaagaagccaaacctactgagcctgagaattaactaggttcttttggatctttggccctgattcaatagtcagatttttgtggtgctctgcaaagagggcatttttcagcttttcttgcaatggatttggaatggacaatatgagctgtcgccacttcataattaccaaccaaagccaaaagatctgagcctgccttttctttatttctttaaattgtttttctttcttactgcctttatctattttaagcaaagtggtcggttgaaacaatggataattcacatttaaatcataagaatctttttcaagtgttcattacatccgttttggttcgtttaaaatattgtttcctatgcgctcctagatgggatacagtacaagtattcaactgttgagcagagatttttacctcaaaaaattagt
+agacacaacatcatagaaacagatcaacaacacattaaaattagcatggatcatagcttacgttgttttgggtcgacactacccaaaactcttcttcagtttctgttatcaccttcactccttctcttcatctccttcttcagtttctccaacgcagccttcgacctcgccaccatacccttcaacgatgcctattcacccctctttggggatggcaaccttgtccgctccgccgatggcaacggtgttcaactcctcctcgatcgcttcaccggttctggtttcgtttcttccaatatgtaccagcatggattcttcagcgccaatatcaagctaccatcgaattacagcgctggtatttgcgtggccttttatacatcaaacaatgagatgtttgagaagacacacgatgagttagactttgaattcttaggtaatatagccggaaagccttggaggtttcagacaaacttgtacggcaatggcagcaccaaccgtggccgtgaggagcggtaccgcctctggtttgatccaaccaagggattccatagatacagcattctatggacagctaagaacatcatattttacatagatgaggttccaattagagaaattataagaagtgaagaaatgggagctgattacccagcaaagccaatggcattatacgccacaatatgggatgcatcaaattgggccacatcgggtggaaa

data/spec/data/nucl_seqs_mixed.txt

@@ -0,0 +1,17 @@
+>Mixed_case_sequence
+tGAtaggATAaTtctagAcaaaaCaTTaGCCGaTCAAGTgtcAtCaTGGAAaAgCagCAgggGccttAgTgATACagTggtgAcTGaTcaTGCTtGTTCTGggGAaaCaTGCtcGTaCTAcgCaattgGAgatGtaTTTATtTgTgAaaAgAcTGGAcAagtTcatgTTtGtgAcgaAacAtGTAGGGaagtaGtaatggatCccaCcAACGaGCtttTGgtcTGTACAATAtCTgGccAcTGttTtgacAGaTtgCtaTcaCcTgCTGaAAtgGAGCCtgATGcTGagcAgcAgCaaGgTGgtgCgGCAgAtGaGgCaGAACcGTtTaTGGgAtCtggccgtTttGcAcgGgCttaTttGCTgGGataCaAtTgTgcTgatgaaAaGgAGCTtGaaGcTActTtGaGgTttTgctGATCcCtAtTGgCccTtCtggagtgGATgatctCAtgTctCAgCATTtAcctATTtaAGatCAAATAAATcgGgtTtccTTTTcGTgtttcTCTtggCAtaaGAAtGTtTGAtTagATCtagAttatgaAaCtcTAAtcgTCTtcTATattaATAATtgtaTgCTTaAATttAtaGTtGaAAtTCCattGAtGaatTTTTCTt
+cagAaGACaTGtctTTgacAAAGGTaTaCCAtcTtttCcncCaacTTGGTTTgAGACATtTATTtGTTGtaccTCgTcCAtCgCGTGTgctTGgTtTGATaACCaGAaaagAtttGtTgaTTGaGGAcACagATGcGAATacATtaGAGcTtCAGgCAaCTagTagtTcgGcaTcCAGGTaAAAGATtgAtggCaAggAATgcaGatgtggagAgcCctcTGCTaAaTggtcTTctGGttCAGaaTCAGATacCtgaCTAataccgtctgCAGcCttcCCgAattcCtTtTTGcGTcCcaTtTTcACttGAaaaTCaTTctTTAttattTttgtAttAATgTTgaAATaggtTaGAgaaCCcgAtattTtGGGGaTGGaacgGggTTgTAgaCtgacaGTATacCctAGaAttTtGTAtAtAAaGtATaAactAcAGCAaGCacagAAaAAaAtCaTGaAaGCGCcCTtgtGATAaTtATgatAgCagaattTAgAcTgaT
+ctcTcTCtcTCtCtCtcTctCTCTCtcTcCGtCGTcgTTTtGGgTtCTgCggatcGgtGGATtCtgGtcGcgAAttCCGACGctGttCGTggcgGcGAACCgaATTCCGgtcaaCaaGcGaagAaGatgaaGgttTTCgtCAAGACtCTgaaGggcTCTcaCTTcGAaatcGaAGTcaAGCcCCAAGACaCgGtttCgGatgtGaaGAAAaAtATtGaaactGtTCAAgGTGgaTgtctATcctgcCgcgcagCaAAtgCTTatTCatcaagGGAaAgtTcttaagGATGGTActaCCTtGgAGGaaAATaAagtAGCTGaaaatagTtTcattGTgattATGATttcCAAGaGtAAGaCTCcGTctggtGaAggaTctaCtaCtTcAGCtgCacCTtCAgCtAAGGCTCcagCTCCtgcTCcTaTATcTTCgggCACGGcTgtgGaaggttcTgATGTCTATGgaCAagcAgCatCcaAtcTggttgctGgTAgCaacTtGgAAgacaCAAtTcAgcaAATtCttgaTGtTGGaggAGgGACCtGgGatAgGgAtAcTgtaGtCcGGGCTcttCGAgCTgCcTTCaacAaccCTgAgaGagcTATTgAaTaTttaTATtcAggAaTccCcGAgcAagcTgaaGcTCCAcctGTGGgCCgTGTGCcTGCaAgTGCacaaCCtGCAAATcCTccagCAGctGCAgctcCgCAaGcGgcAcAAccTgctCctgTTACctcAagTGgGCcTaATgCTAaTccTTTAgaccTTtTTCCacagGgcCTCccAAatgTTGgtTcTggtggTGcTggTGctggTGCTggcTCtttAgattttcTtcGcAACAGccAACAAtTcCaaGCcTtgcgagcTatggtGCagGCTaATCCaCAAatattGcAGCCTaTgcTaCaaGAGCttGgcaaAcAGaAtcCtCatcTAatgaGattgAtTCGagAtcATCAAGcTgACttCCtTcgcTTgatAAATGaGCcTgtGGaAgGtggcGAaggGaAcCCattgggGcagCtggCTgGtgGcAtACCACaAGCaATAacTgTCAcCCctgAGGAGcGCcAagcAATtGAACGTCtTGaaGcAaTgggTTTCgAtCgtGCgatTgTatTGgAGGTgTTCttCgcttgcaaCAaAaaTGagGAATtGgcTgcCAACtaccTTTtAGaTCAcaTGCatgAgtTcgACgaACaaTAaatCtCttcaTGTtGcTAaattATTtAtCTgttatcttTtTAAtgTtTaTGgGgcCTTtGTtttActAgACGgtTtGatgAGGTAaTaCTtGAAaaTGAAaaAAaTCtcAagTGgAGAaggaAcGTTTTTAccACcTCCACaTTAtTgCCtTTgTGGACagtcTcagTaTtcATataCATaGTCgTTtgtcctGtActATtGgtAtTgTGCaTcCttttAACAtgTGTaaTTgtTtaGcTgcgCaTCctATTCTATaTttTCT
+CGttcGcaTTGttcacTcACCaTACgcACTtCCAttttCATcTCccaCCgtCGCATTtTcTTCGgatCTgaAaTtcctCAcCaTGAatCGCcACCacgAtCccAAtCCaTtCGaCGAAGACGaaGTCAATCcctTctCgAAcGgtGctgctCctGGaTCTaaATcaCgtAtTCcAcCaTtGGcAtCcgaacCacTGgGCtTTggTCAaagacaTgATgctACAGTTgAtattcCtTtGGaTACcacaaATGaGCCTAaaAAAaaAGgtcaagAgctaGcaGCTtgggAAGcagaTttgAaaaGGAGagAaaAggatTTAaaaaGAaGagagGatGCtgtTTcTaGagCtGGTgtGCCTGttGatgAtAagaATtggCctccGATTTTccCAAttATtcAcCATGAtAtTGCCAatGagatAcCggTTCatgctCAgAGGctgCaAtAtTtgGCctTTGcaagTtggTtAGgAATtGttctCTgcCttGTtTTTAAtGtagTtGCTGtGatGgtctGTTgGatCagaggcggTggtgttAaAaTttTttTCcTTgCGGtgaTcTAtGCtctACTTggTGttCCccttTcATaTGtgCTTtGgtaCagGccCCtTTAtCgtgCtATGaggacGgATaGtgCaCtgAaGTTTggctGGTTtTTCaTgTtcTactTGctTCatattGCaTTtTgCatCTTTGctGCaATtGCAcctccagTtGTTTTTcaTGGgaaatCatTaAcGggCatCcTTgCAGCaActGACgtctTcTcAgAccatgtaTTGGTTGGgatAtTcTATtTGgTTGgaTTtgGcCTgtTtTGCTtgGAgtctCttctAaGCttgTggGTaAttCagaAaAtAtacctgtTTTtCcggGGgcATaAgtGagGCtactcaGgAttttGATccATcgGctTTTatgAtAtcaGtCActtCccGgcGtggCTTAGtATattCtTTctTtTtgTCTAtcCTCtTTtTTcGcttgCAAtaTttTcGtGtGatATTGttTgTTgTTgTagtCTAgTtCTTGtTAcaGagcTtAgTGtgtAaTTtccTgTgTaATGAaTtCtGTgAagTtTaGTaATTttctAGTgtAAcAATaAccaaGctttgctTTCGataaGcaTataTgtAGtgGATttCcataaGgAATtAtTGtAgtGcTATTgtAgttgtGaAtagtgACaCccctCGGAgGTTTtCTattTGTaaGaCaGcactgaTGcaAACaCTtTAgTtAaAAtTcAtGtAGgAtcTATTcaaTt
+CaGgatAcACctccAgAtgGgGAAaATatgaCaggAgCctCCaaagAGATgAAtgTaGaaTcTattCcTtcCTTctttCaAgataTTATtGagCgTATggttTcCtCaCAagtTAtGACtGtGaAGcCTgATGcttGCattGtggAtttctaTAaTgaGggCGatCaCtcACATcCCTacAAttGgCCacATTggtATgGAAGgCcTgtcTATatCCtTTCcCtGaCAGAaTgTGATAtGAcTTtAgGaaGAgTAATTTCCtcagacCaTccAGGGgattAcAGgggCTCtCTGaAGCTTtcTcttcTccCtGggtCtCTtctGtCaAggcAAGGgAAATctACtAattTtgcTagAtatGCtAtTcCTtCtATccgcAAAcAAcgCaTacTTgTTAtTttTaCaaaGtccCaACcAaaGaaGtcacTGtcAAGTGaTGCTcaACGTtttaCcTcatcagCaGcaTCTTcTCatTGggGtCcaCCgCCAAgCcgTtCcccCAaTcACgTtcgtCatcAtttAGGCCACaAGCatTatgCtTCAgCtcCAAcaaacGGAggActgcCAGCtcCACCAATCCgGccacA
+aaGGAcTaGTTGAttTGCtACatGTgtTctgtgtTgtTctTGCTttGGtAaATGTGtctCTAgTGAAAgcaGaAgaTCcatAcaagtTCTacacATggACAGtgACttAtGgaAcTCtttcTcctcTgggcaGtcCTcAAcaaGTTATtctGATcAaTgGTCagTtTcCtggtcCAaGACtTgACTtGgTaACTaaTgAcaaCgTgatTCTCaaccTCAtCAacAaGCtGgATgagcCATTcttgCTCaCatGGAATGGCaTTAAGcagAGGaaaaaTTCTTgGcAaGaTGGgGtttTagGaActAAcTGtccCATtcCTCCAaacTCAAaTTACaCtTaCaAgtttcaGgCCAaggatcAgATtgGCactTatacatacttTCCAtCaAcTaaGATgCaTaAaGctTCTGgaGggTttGGaGctctcaATgTtcttCatagATctgTcATCCcaaTCcctTaTccAAAccctgaTggaGATtttaCATtaCtCAttGgTGAtTgGtACAAAActAGccaCAAgaCATtAAgCcaAAcAttGgAttCtGGGaAaTctcttgCCtttCCTGATGgcctCCTtaTCaatGgcCagGctcATTCtaCctTCaCTGTTAaCCagGGAAAAaCctATAtgTtcagGaTcTCAaaTgTTGGtCTgtCaACctcaAttAaCTtcagaATtCagggAcAtAccCtAAAACtAGTTGAGGtTGAaGgatCAcAcaCtatccagaacgAATaCGActCGcttGaTGTgCaTgttgGCcAaTcaGTTtCtgtgttAGtAaccTtAAATcaaCCTcCaaaGGaCTatTacaTCgTtgcctCaACAAGATtTACCAagaCtgtTctCaCTaCaaCctCAgTgCTAcAcTaAAAttctcAgtCagcCgcATcaggatccttGCcTgcTCCcccTGctGaCAaT
+aTtgaaATaCGtCTtgCAaaAGctgaagcTATtaatTggaCatCtCTcGAaTATaGcAaggATaTGcctcCcCAaaaaATTaaAgTGcctACaATtcAAtCtGaaaggCcTgCAtACccAtcAtCAaaGCcaAGGACaaaagAtTgGGATaAgTtGGaAGctAtgGTGAAAaaagAggAgAAagAagAaAagctgGATGGTGATgCtgcTTtgaATAAatTGtTCcGtGATAtTtAtCaaaATGcTgAtGaGGacAtGCGGAgAGCAAtGaGcaAGtCaTttctGGAgTcaAAtGGaaCAGtGCtGTCaAcggAtTGgAaagAaGTGgGATccaaGAAgGTGGAaGGaAgTcCTCCaGaAGGTATGgAATtgaaGAaaTggGaGTaCtAaTTcagtacAagCtgAtgcTcaTgaGagtTCAAAttCAcaaaAataaatTctgAGAAgggAAaCAAatTCTgtaaTcTtaAtGgtaTcGGTtAttTTg
+TgagATcaTGcgcgAaAtgATGaGGAAtacAgacaGagCCATGaGCAAcaTtgAGtcTtCtcCTgaggGATtCAaCatGcTGAgGcGCATgTaTGAaAAtGTTcaAgAaccatTtTtAaatgCCactaCAAtGGCTggTAaTACAGGAAaTGATGgTgTCAggaATCaatCaacTaAtccCtcAAcGaCtaAttcTGaaGCAacTtCCCCtgTtCcAaATaCtAAcCcACttcCTaatccTTggTCctCcACTgGaaCTGgAggtgcACaAGgCaACaCcagAaGGACaacTgcTgGtGGGGATgcTcGgCagCaGgCaCTCaCTGGactAGgaggAcTTggtGTGCCaGatctTGaaggcaTGAtgGGTGGTatgcCaGatCCtgCTatGTtgaccCaATTaaTGcaaAatCCAGcTAtTtCacaaatGaTGCagagtAtccTttCCAatCcACAgacTaTgAAtCagattCTTGGTCTcAATactGAgcaGcGTGGcATGcCtgaTCTAaaCtCaCtaaGaAgaTGtgATGcaaaaCcCAGagTttCttcgcTTATTtTCcTCaCcTgaGAcacTgCAGcAacTcAtgtCTttCcAGCaatcTcTtaTgTcTCAAgtTgG
+cAgcTCTATTctccACcAACaCaAaAAcGctcaCaAaCTagcTTcTTTggaGAAaACATtaGaGACAAtaGtGGCGgTGgTgGgaacaaTGGcAgcCTCactACAAgCagcAgCtACTtTCaTGCAACcaAccAAGtTTGgtcGCaccaaCaCttTGCAGctGaAATCtActCAAtCCATTtCTAAggCTTttGGgTTGGaGcCcTctgcAgcTaAGgtCtCAtgTTCcCtTcAggCTgatttCAaggaGtTGgCTCAcaAGtGtgtTgAaGcTaCCAagATtGctgGGttTGCtcTtGCcaccTcTGCtCTagTTgTcTCtgGAGCaAgtGCGGaAGgtgcTCCgaaGAGGCtaacCTtCGaTGAAaTCcagaGcAAgACaTacatGGaAgtgaaGgGaaCCgGaaccgCAaaccAGTgCcCcAccattGAaGGggGaGTGgaAtcattttCCTtcaAGgcCGGGaAGtacAATGCcAagAagtTCTGCCttgaAcCcaCtTCAttCacagTgaagGCAgAgggaGtAgccaaGAaCgcCCcacTTGagTTCcaaaaCAccAAGcTCATgaCACGTcTgAcCTacACCctCGacGAgATCgAaggaCCctTTGAgGtTtcctctgatgGCactgTcAagTTCgaGGAGaaAGAtGgCaTTGActAcgCtGctgTCacagtTCagcttCCcGgTgGcGagcgtGtTccAtTcctTTTcAcCAtCaaACAgTtggTAGcAtCtGGgaAGccAGAcagcTtcagtggGGagTtTcTAgtgCcTtcaTACcgtggAtCttccttcttggACCccAagggaaGAGGTGCgTCAACTGGtTAtGacAAtGCTgtcGCaTtgcCTGCtgGtggcAgaGgagATGaGGAaGaaCTTgCTaaGgAgAacAacCAGAgtgCTtCTtCatCccaAGGGaAgatcaCCttGaGcGtgAcacAGAgCAAgccTGAtaCCgGTgaGGTgaTtgGTGTGtTcGAGAGCaTTcagCcgTCCgaCaCtgaTTtgGgaGcgaaAgctccCaAggAtgtGAaGATCcAggGAgTtTGgTATGCtcagctCGaGTCatagaCAgctTtATCTcTcttcTgcTttaTtTtGtAttttGTTGTAaCtTCtcaGtGTTgCTgcCaTtAccttTGacAccaCtgtCCcAGCATGAGAgtGttAtCctTGtttgTAtGtatacTaTCGActTtCAattAtaatgCTCgAAaaTGTccAaggTtt
+aGcagTGTtcCcATGaaAccTtcccACtGAgtCAaCTcACTCtgTAcAtAaAacccTCttcAtCATCaTCATgGCTtCtCAaGTtttTCTtcAgcAAggGtTgttActgttTGCCCcAaacCAaTgttCtccaAcCaAgctcGgtGtATcTtCTtGCctCggtTCtCGTaAcTttCCGttGaTttCCtccaCctcAatTtCAtGGCGTtgcaacaAccCtcTcTctGCcaAACCctctTTtGTtgtCaGagCTgaCtcCaatgtcgaCGcTGcttcCGACaatgctGGtGAaGttCCAGaAGctGAAGGTaGCGtTGaTcaGGttCctGaagaTGGaGAagCaGAAcTaGcttCggAttCtGaGGTGgAgCAacccaAGcCCCCtAGAAAgCAACGaGtcaaGcTTGGAgatgttatGGggaTAttgAatCagaGGGcAaTtgagGCaTCggaAaGCatGAgGCcGACTCcAgaAATTaggaCtgGAgaTgTTgtGgAAaTCAaaCtgGaAgttcCTgaGaacaagCGtAggTtGTCtatttaTAAaGgTAtAgtcatCtCAAgAcAAaatGCtGGTAttCacacAacTAtTcgaaTcCGAaGgaTTaTTGcTGGcACagGGGttgagAtTGtcTTCCcAAtttaCtCacCaaACATcaaagAaaTCAAAgTGgTaaAccacCGtaaagTcAGAaGAGCAAgAtTGtaCtatttAAGAgacAAgCtTcCCAGattCtccACttTCAAatGaTAcgGttACCaCttCTCaTCCtGaTcttcttcAaaGTagTTGCTgATatTGCaGGgccaTATTtTGgttaTttcGtTTTGtTgTGtTgTaGaaTATaTcAtTtTtCtTCcTctaAATCtAtcCtCCgAGAaTtGGaaAcAagTGtAtgtAtgTTgCCctTGaTaATaTtTgAaAtttGAagTgtTctcCCtTgcATtccTTGGtatAGGatAGAaAgccaAgCTcCTaAAcAAACaTtACTAaATatgacAgTctaAggaaTGAgcATGtGtATCgAtaCCaGtTaAGTGCatTGTgAATgtATTTTttttTTttATCtCtatcCatAaAaAaaGgtaTgTTCAtTCttg
+aAgaaAcAaGagAgAgAAGATgAtTTagAtgagccAAaAAcaaaGGAAaAacGGcaaAAGgGaGaGAaaGGaaaATCTcCatcAgGTTttCTTgCtcCtctcCaGctaTcTgAtgCcCttGtaaacTtccTTgGtacTgGAgaAaGTGaattATcaaGAtctGaTGTCATaAAaAgAATgTgGGAAtaCatAAAagGAAacgaCcTTcAgGaTCCttCtGAcAAgAggaAAatATTATgCgACgacaaGCTGAAaGAACtCTTTGAtgTgGacTcCtttAacGGcTTCaCcgtTacAAAacTgTTGaCtcCTCaTtTtAtAAaggCAGAGcAgTGaGTTgcTTGtGgaaATcGgTAatGTtGtccaAtTAGGttTGgaaggtCcTTcTTTTGTggCCTtTtggcatTGTcTGCCaAcAcgAgGAATaggAatTAggAAcatGacagaTTTTCAGtaAatTTTtCtCcAaGAatTtaatGtTaCGtGACCATTaCTTTGTTTTTTTtaaTatCACgTTTtGTcactTGgcagTTGAAATttttgtATAtTtTCagtTCcTGaagcTgcAaGgAtAaTGcTgaCTTctTaCtcTACTcTgcAtTTgCtCaTaTgAggCACtacaCatatCcataatACAtGaATAAaTTtgCAgTAtTGaA
+CATTtgtTccATtTGctCAggcaTTtgCagcTGtAcTtACagCTgTCCTtaCtgGTTCTCtctaTtATgTGGCtgcCtcTcCTAAagaTcCtActtATAttgtgGCaCcTGTTtTAcagTCTcGCtCTGGtcgTcaagattTgaAaAaGCTatTtgAAGCcTgGTaTGaGaAacGgCAaatGaaaaaaATATAttcACcaCTtctgGaaGgActaCtagCTcTcTacctAggatttgAgTggaTcCaAacgAaTAAcatTCTtgCtccCattatcacACATGGCatatacTccacaGttaTAttGGGACaTgGcctTTgGAagATAAAcGacCAcCGGCgaAgacTaCGTcAaaGAATCcAACAgctCAAATctGAAGaACAaAAttcCCAgtagActttgAAATAccttCCatgtcTggctGTgatacAAAaaaTgtAtATGtaTGTattagagcTGCtAATtatgtaAagAGaaaagATGtATataCtTgtgTtaGCTgAGGTCtCgTAcaCacTGaatATTcaGGTTtTgttCAcCAttTTcTaAtTTcgaGttACTATATgTAgTGTTTTctaataAAATGaaaTAaaatccCcAagttGgGttGAtTTAaatt
+gaGaCctgtTATgaTtcAcaGaGccaTTCTaGGaTctGTtGaGCgcAtgTtTGCCATtcTtTtAGaGCaCTAcaaGgGTAAAtGgCCCtTGTggcTCagtCCtCGTcAAgcAATTGtATGtCCtgtgTcAGaGAAatCacaAgCtTAtgcActgCAGGtGcgAgAtcAgATCcAccAAGCAgGAtaTCAcgTTgAtGCTGatACAACTgatCgGAAGaTTCagaAGaaGGTaCgGGAaGcTCaaTtagcGcaGtAcaACTaCATCTtggTtGttgGagAGGaGgAAGCtAATaCAGgaCagGtgAGTgtaCGGgtTagaGATaaAGcAgaCcaTAGCgttATGAGtATtgAgAaTCtacTCaAAcAcTtCAGcgACgAaGtTGCaGCtTtTCAtTgAtAcTtCtctTgTGAaAACTGTtgGaaGCAaATTTTaCCCCcacTCaCcTAGtTtgTtcAcAcTttgtGtgcaTTaTTtaTATTttCaGcCtGACaaTtTacAtTtAGATgaTTTGGgtaatgACtgTaTtTtctAtGTgaAtTttgGaGcgCACtGATAtCGAtCCaTtGttTgaaAAgCtgagAgAaAgtGTAatCTttTatTTTctgTCTACAtttTaAttAtgTTTTTcgTTagtTtTTtcctTTTatATaTtTgttTGTtaaaTtgaAgGaaAcTattgTtgG
+ggCaccAgGgATcTtaCaaGgcTggatCtccataATaaCAaGTTGaCaggGccTatTCctCctcAaaTtGgACggTtgaaGCGtCttaAAATACtcAAtTtGAGgTGGaAcAAAcTacaGgatGCAAttCcTccaGAAaTTggcgaGcttAaAagTttaacaCATctgTAccTAagcTtcAATaGTTTcAagGGagaAaTtccCAaagAgCtagCAAATctTCcAGACcTtcGCTAcCtttaTCTtCATGAaAaCCGtttAATtGgtaGGAtAcCACcTgAGTTgGgCACTCtAcaAaaCCttCGGCacttGGATgCtGgtaacaATCAtttgGTgGgtAcCatAagggAActcaTTcGtATtgAAGGTTgctTtCCAGCaCtcCGcaatCtAtatCtaaacaATAatTAttTtAcTgGaGgAATGCCtgcaCaactTgCcaacTtATCcaGtCtTGAgaTcTtgtAccTgtCCtAcaAtAaaATgtCAGgAGtTATAcCaTcTagcCttgcTcATatTCctAaaTTGaCATACTtGTacTtGgAtcacaatCagTttTcGgGGAGaattCCCGaAccCTTtTAcaAACaTtCaTTtTtGAAagAaATGTAcatCgAGgGaAAtGCattCCGGcCtGgtGTtAAACcCaTTgGtTTCcAtAAAGTgCTTgaAGTtTctgAtTCAGACtTccTTGtTTaatgAaActCaACAtAtTTaGtttTTTagGAAGTttAcGtGtaTAATTaatgAAacAataGCtCCtctgatTTtctcAatgAAAAtTgctATATGGgTaatTCaatTtttgtCAcGGCtGtCttgTcagaAGaAtcAATAAaTAatAgTGttTTTtaaCtCt
+GgAaAtGAgcACAaTgttAaGCAGATcaaGaAttAccgCCAaAAgGTtgaGgAgGaACTctcCaAAaTttgTggtGacatcCtgACtattaTAgacCaGcAtCTAATTCcTTctTcCgcCtcagcagAAGcTaGtgTttTCTActaTAagAtGAAAggtGAttatTaTCGGTATcTtGCtgagTTCAAgAccgACCAAgAaAGgaAagagGCAGCCgagcagtcAcTcAAGGgatAtGaggCTGcTtcagcCaCtGcCaacaccgatCTtCcATcAAcaCAtccAAtcCGTCtTgGaCttgcTCtCAaCtTCTCtgTcTTtTAtTaCgaGatCAtgaaCTcTcCTGAaaggGccTgccAtTTGgCTAAacaagCTTtTGATgagGcAATtgCAGagTtggAcaCCttgagTgAAGAGTcatACaaggACaGTactttGatcaTgcAgTtGTTgAGaGACAACCTGaCtcTctGgaCaTCCGATTtGCcAGAaGatGGAgGcGAGgAgAAcAtaaAAgCTGAagaagccaaAccTACTGaGccTgAGAattAAcTaGGtTcttTTgGaTCttTGgCcCTgattcaatAGTcaGAtTtttGTGgtGctCtGcaaagaGggcaTTTtTcagcTtTtcttgcAatgGaTTTgGaatGgacaatAtgAgcTGtcgccActTCaTAaTTAccaaccAAaGcCAAaagATCTgaGCCtgcCTTTTctTtAttTctTtaaATtgttTtTCttTCtTacTGCCTTTatcTATtTtaAgCaaaGtggtCgGTTGaaacAaTggataATTcacaTTtaaAtCaTAagAatcTTTttcaagtgTtCatTAcATCcGtTTtggttCGttTAaAAtaTTGTTtcCTAtGcgcTcctaGaTGggATAcAgtACaAGTATtCAactgtTGAGCAGAGAttTTtacCTCaaAAAAtTagt
+agACacAAcaTCATAgAaacagaTCAAcaaCAcattAaaaTTagCaTgGAtcATAGctTacGTTgTTTTgGgTcGACACTacccAAAacTCTTCTTCAGtttCTgTtAtCACcTtCAcTCCTTCtcTtCatctCCtTCTTCagtTTCTccaaCgCAgcCTTCgAccTcGCcACcaTACCcTTCaacGATGcCtaTTcacCccTcttTgGggatGGcaaCctTgtCCGctccgCCGATGgCaACGGtgtTcaActcctcctcGAtcgCttCaCcGGttCTGGTTtCGttTcTtCcAATAtGTacCAGcATgGAtTCtTcAgcGCcaAtaTCAAgctACCAtcgAATTacaGCGctGgTaTtTGCGtGgCcttTTaTACatCaaaCaATGaGatGtTtgaGAagacAcaCGaTgAGTtagaCtTTgaaTtcTTaggtaaTATagCCGgaaAgccttGGaggTTTcaGACAaActtGTaCggcAatgGCAGcAcCAacCGtGgcCgtGagGAgCGGTaCCgCCtCTGgTTTgATcCAACcAaGGgATtCCATaGaTaCaGCATTCtaTgGaCaGcTAAGaACATcaTATTttaCaTagAtGAGgTtcCaAtTagagAAATTaTaaGaaGtgAaGaaaTgggAGcTGATtaCccagcAaagccaATGgcAttATACgCcaCaATATgGGaTgCatCAaATtGGGccACAtcGgGTgGaaa

data/spec/data/nucl_seqs_upper.txt

@@ -0,0 +1,17 @@
+>Uppercase_sequence
+TGATAGGATAATTCTAGACAAAACATTAGCCGATCAAGTGTCATCATGGAAAAGCAGCAGGGGCCTTAGTGATACAGTGGTGACTGATCATGCTTGTTCTGGGGAAACATGCTCGTACTACGCAATTGGAGATGTATTTATTTGTGAAAAGACTGGACAAGTTCATGTTTGTGACGAAACATGTAGGGAAGTAGTAATGGATCCCACCAACGAGCTTTTGGTCTGTACAATATCTGGCCACTGTTTTGACAGATTGCTATCACCTGCTGAAATGGAGCCTGATGCTGAGCAGCAGCAAGGTGGTGCGGCAGATGAGGCAGAACCGTTTATGGGATCTGGCCGTTTTGCACGGGCTTATTTGCTGGGATACAATTGTGCTGATGAAAAGGAGCTTGAAGCTACTTTGAGGTTTTGCTGATCCCTATTGGCCCTTCTGGAGTGGATGATCTCATGTCTCAGCATTTACCTATTTAAGATCAAATAAATCGGGTTTCCTTTTCGTGTTTCTCTTGGCATAAGAATGTTTGATTAGATCTAGATTATGAAACTCTAATCGTCTTCTATATTAATAATTGTATGCTTAAATTTATAGTTGAAATTCCATTGATGAATTTTTCTT
+CAGAAGACATGTCTTTGACAAAGGTATACCATCTTTTCCNCCAACTTGGTTTGAGACATTTATTTGTTGTACCTCGTCCATCGCGTGTGCTTGGTTTGATAACCAGAAAAGATTTGTTGATTGAGGACACAGATGCGAATACATTAGAGCTTCAGGCAACTAGTAGTTCGGCATCCAGGTAAAAGATTGATGGCAAGGAATGCAGATGTGGAGAGCCCTCTGCTAAATGGTCTTCTGGTTCAGAATCAGATACCTGACTAATACCGTCTGCAGCCTTCCCGAATTCCTTTTTGCGTCCCATTTTCACTTGAAAATCATTCTTTATTATTTTTGTATTAATGTTGAAATAGGTTAGAGAACCCGATATTTTGGGGATGGAACGGGGTTGTAGACTGACAGTATACCCTAGAATTTTGTATATAAAGTATAAACTACAGCAAGCACAGAAAAAAATCATGAAAGCGCCCTTGTGATAATTATGATAGCAGAATTTAGACTGAT
+CTCTCTCTCTCTCTCTCTCTCTCTCTCTCCGTCGTCGTTTTGGGTTCTGCGGATCGGTGGATTCTGGTCGCGAATTCCGACGCTGTTCGTGGCGGCGAACCGAATTCCGGTCAACAAGCGAAGAAGATGAAGGTTTTCGTCAAGACTCTGAAGGGCTCTCACTTCGAAATCGAAGTCAAGCCCCAAGACACGGTTTCGGATGTGAAGAAAAATATTGAAACTGTTCAAGGTGGATGTCTATCCTGCCGCGCAGCAAATGCTTATTCATCAAGGGAAAGTTCTTAAGGATGGTACTACCTTGGAGGAAAATAAAGTAGCTGAAAATAGTTTCATTGTGATTATGATTTCCAAGAGTAAGACTCCGTCTGGTGAAGGATCTACTACTTCAGCTGCACCTTCAGCTAAGGCTCCAGCTCCTGCTCCTATATCTTCGGGCACGGCTGTGGAAGGTTCTGATGTCTATGGACAAGCAGCATCCAATCTGGTTGCTGGTAGCAACTTGGAAGACACAATTCAGCAAATTCTTGATGTTGGAGGAGGGACCTGGGATAGGGATACTGTAGTCCGGGCTCTTCGAGCTGCCTTCAACAACCCTGAGAGAGCTATTGAATATTTATATTCAGGAATCCCCGAGCAAGCTGAAGCTCCACCTGTGGGCCGTGTGCCTGCAAGTGCACAACCTGCAAATCCTCCAGCAGCTGCAGCTCCGCAAGCGGCACAACCTGCTCCTGTTACCTCAAGTGGGCCTAATGCTAATCCTTTAGACCTTTTTCCACAGGGCCTCCCAAATGTTGGTTCTGGTGGTGCTGGTGCTGGTGCTGGCTCTTTAGATTTTCTTCGCAACAGCCAACAATTCCAAGCCTTGCGAGCTATGGTGCAGGCTAATCCACAAATATTGCAGCCTATGCTACAAGAGCTTGGCAAACAGAATCCTCATCTAATGAGATTGATTCGAGATCATCAAGCTGACTTCCTTCGCTTGATAAATGAGCCTGTGGAAGGTGGCGAAGGGAACCCATTGGGGCAGCTGGCTGGTGGCATACCACAAGCAATAACTGTCACCCCTGAGGAGCGCCAAGCAATTGAACGTCTTGAAGCAATGGGTTTCGATCGTGCGATTGTATTGGAGGTGTTCTTCGCTTGCAACAAAAATGAGGAATTGGCTGCCAACTACCTTTTAGATCACATGCATGAGTTCGACGAACAATAAATCTCTTCATGTTGCTAAATTATTTATCTGTTATCTTTTTAATGTTTATGGGGCCTTTGTTTTACTAGACGGTTTGATGAGGTAATACTTGAAAATGAAAAAAATCTCAAGTGGAGAAGGAACGTTTTTACCACCTCCACATTATTGCCTTTGTGGACAGTCTCAGTATTCATATACATAGTCGTTTGTCCTGTACTATTGGTATTGTGCATCCTTTTAACATGTGTAATTGTTTAGCTGCGCATCCTATTCTATATTTTCT
+CGTTCGCATTGTTCACTCACCATACGCACTTCCATTTTCATCTCCCACCGTCGCATTTTCTTCGGATCTGAAATTCCTCACCATGAATCGCCACCACGATCCCAATCCATTCGACGAAGACGAAGTCAATCCCTTCTCGAACGGTGCTGCTCCTGGATCTAAATCACGTATTCCACCATTGGCATCCGAACCACTGGGCTTTGGTCAAAGACATGATGCTACAGTTGATATTCCTTTGGATACCACAAATGAGCCTAAAAAAAAAGGTCAAGAGCTAGCAGCTTGGGAAGCAGATTTGAAAAGGAGAGAAAAGGATTTAAAAAGAAGAGAGGATGCTGTTTCTAGAGCTGGTGTGCCTGTTGATGATAAGAATTGGCCTCCGATTTTCCCAATTATTCACCATGATATTGCCAATGAGATACCGGTTCATGCTCAGAGGCTGCAATATTTGGCCTTTGCAAGTTGGTTAGGAATTGTTCTCTGCCTTGTTTTTAATGTAGTTGCTGTGATGGTCTGTTGGATCAGAGGCGGTGGTGTTAAAATTTTTTTCCTTGCGGTGATCTATGCTCTACTTGGTGTTCCCCTTTCATATGTGCTTTGGTACAGGCCCCTTTATCGTGCTATGAGGACGGATAGTGCACTGAAGTTTGGCTGGTTTTTCATGTTCTACTTGCTTCATATTGCATTTTGCATCTTTGCTGCAATTGCACCTCCAGTTGTTTTTCATGGGAAATCATTAACGGGCATCCTTGCAGCAACTGACGTCTTCTCAGACCATGTATTGGTTGGGATATTCTATTTGGTTGGATTTGGCCTGTTTTGCTTGGAGTCTCTTCTAAGCTTGTGGGTAATTCAGAAAATATACCTGTTTTTCCGGGGGCATAAGTGAGGCTACTCAGGATTTTGATCCATCGGCTTTTATGATATCAGTCACTTCCCGGCGTGGCTTAGTATATTCTTTCTTTTTGTCTATCCTCTTTTTTCGCTTGCAATATTTTCGTGTGATATTGTTTGTTGTTGTAGTCTAGTTCTTGTTACAGAGCTTAGTGTGTAATTTCCTGTGTAATGAATTCTGTGAAGTTTAGTAATTTTCTAGTGTAACAATAACCAAGCTTTGCTTTCGATAAGCATATATGTAGTGGATTTCCATAAGGAATTATTGTAGTGCTATTGTAGTTGTGAATAGTGACACCCCTCGGAGGTTTTCTATTTGTAAGACAGCACTGATGCAAACACTTTAGTTAAAATTCATGTAGGATCTATTCAATT
+CAGGATACACCTCCAGATGGGGAAAATATGACAGGAGCCTCCAAAGAGATGAATGTAGAATCTATTCCTTCCTTCTTTCAAGATATTATTGAGCGTATGGTTTCCTCACAAGTTATGACTGTGAAGCCTGATGCTTGCATTGTGGATTTCTATAATGAGGGCGATCACTCACATCCCTACAATTGGCCACATTGGTATGGAAGGCCTGTCTATATCCTTTCCCTGACAGAATGTGATATGACTTTAGGAAGAGTAATTTCCTCAGACCATCCAGGGGATTACAGGGGCTCTCTGAAGCTTTCTCTTCTCCCTGGGTCTCTTCTGTCAAGGCAAGGGAAATCTACTAATTTTGCTAGATATGCTATTCCTTCTATCCGCAAACAACGCATACTTGTTATTTTTACAAAGTCCCAACCAAAGAAGTCACTGTCAAGTGATGCTCAACGTTTTACCTCATCAGCAGCATCTTCTCATTGGGGTCCACCGCCAAGCCGTTCCCCCAATCACGTTCGTCATCATTTAGGCCACAAGCATTATGCTTCAGCTCCAACAAACGGAGGACTGCCAGCTCCACCAATCCGGCCACA
+AAGGACTAGTTGATTTGCTACATGTGTTCTGTGTTGTTCTTGCTTTGGTAAATGTGTCTCTAGTGAAAGCAGAAGATCCATACAAGTTCTACACATGGACAGTGACTTATGGAACTCTTTCTCCTCTGGGCAGTCCTCAACAAGTTATTCTGATCAATGGTCAGTTTCCTGGTCCAAGACTTGACTTGGTAACTAATGACAACGTGATTCTCAACCTCATCAACAAGCTGGATGAGCCATTCTTGCTCACATGGAATGGCATTAAGCAGAGGAAAAATTCTTGGCAAGATGGGGTTTTAGGAACTAACTGTCCCATTCCTCCAAACTCAAATTACACTTACAAGTTTCAGGCCAAGGATCAGATTGGCACTTATACATACTTTCCATCAACTAAGATGCATAAAGCTTCTGGAGGGTTTGGAGCTCTCAATGTTCTTCATAGATCTGTCATCCCAATCCCTTATCCAAACCCTGATGGAGATTTTACATTACTCATTGGTGATTGGTACAAAACTAGCCACAAGACATTAAGCCAAACATTGGATTCTGGGAAATCTCTTGCCTTTCCTGATGGCCTCCTTATCAATGGCCAGGCTCATTCTACCTTCACTGTTAACCAGGGAAAAACCTATATGTTCAGGATCTCAAATGTTGGTCTGTCAACCTCAATTAACTTCAGAATTCAGGGACATACCCTAAAACTAGTTGAGGTTGAAGGATCACACACTATCCAGAACGAATACGACTCGCTTGATGTGCATGTTGGCCAATCAGTTTCTGTGTTAGTAACCTTAAATCAACCTCCAAAGGACTATTACATCGTTGCCTCAACAAGATTTACCAAGACTGTTCTCACTACAACCTCAGTGCTACACTAAAATTCTCAGTCAGCCGCATCAGGATCCTTGCCTGCTCCCCCTGCTGACAAT
+ATTGAAATACGTCTTGCAAAAGCTGAAGCTATTAATTGGACATCTCTCGAATATAGCAAGGATATGCCTCCCCAAAAAATTAAAGTGCCTACAATTCAATCTGAAAGGCCTGCATACCCATCATCAAAGCCAAGGACAAAAGATTGGGATAAGTTGGAAGCTATGGTGAAAAAAGAGGAGAAAGAAGAAAAGCTGGATGGTGATGCTGCTTTGAATAAATTGTTCCGTGATATTTATCAAAATGCTGATGAGGACATGCGGAGAGCAATGAGCAAGTCATTTCTGGAGTCAAATGGAACAGTGCTGTCAACGGATTGGAAAGAAGTGGGATCCAAGAAGGTGGAAGGAAGTCCTCCAGAAGGTATGGAATTGAAGAAATGGGAGTACTAATTCAGTACAAGCTGATGCTCATGAGAGTTCAAATTCACAAAAATAAATTCTGAGAAGGGAAACAAATTCTGTAATCTTAATGGTATCGGTTATTTTG
+TGAGATCATGCGCGAAATGATGAGGAATACAGACAGAGCCATGAGCAACATTGAGTCTTCTCCTGAGGGATTCAACATGCTGAGGCGCATGTATGAAAATGTTCAAGAACCATTTTTAAATGCCACTACAATGGCTGGTAATACAGGAAATGATGGTGTCAGGAATCAATCAACTAATCCCTCAACGACTAATTCTGAAGCAACTTCCCCTGTTCCAAATACTAACCCACTTCCTAATCCTTGGTCCTCCACTGGAACTGGAGGTGCACAAGGCAACACCAGAAGGACAACTGCTGGTGGGGATGCTCGGCAGCAGGCACTCACTGGACTAGGAGGACTTGGTGTGCCAGATCTTGAAGGCATGATGGGTGGTATGCCAGATCCTGCTATGTTGACCCAATTAATGCAAAATCCAGCTATTTCACAAATGATGCAGAGTATCCTTTCCAATCCACAGACTATGAATCAGATTCTTGGTCTCAATACTGAGCAGCGTGGCATGCCTGATCTAAACTCACTAAGAAGATGTGATGCAAAACCCAGAGTTTCTTCGCTTATTTTCCTCACCTGAGACACTGCAGCAACTCATGTCTTTCCAGCAATCTCTTATGTCTCAAGTTGG
+CAGCTCTATTCTCCACCAACACAAAAACGCTCACAAACTAGCTTCTTTGGAGAAAACATTAGAGACAATAGTGGCGGTGGTGGGAACAATGGCAGCCTCACTACAAGCAGCAGCTACTTTCATGCAACCAACCAAGTTTGGTCGCACCAACACTTTGCAGCTGAAATCTACTCAATCCATTTCTAAGGCTTTTGGGTTGGAGCCCTCTGCAGCTAAGGTCTCATGTTCCCTTCAGGCTGATTTCAAGGAGTTGGCTCACAAGTGTGTTGAAGCTACCAAGATTGCTGGGTTTGCTCTTGCCACCTCTGCTCTAGTTGTCTCTGGAGCAAGTGCGGAAGGTGCTCCGAAGAGGCTAACCTTCGATGAAATCCAGAGCAAGACATACATGGAAGTGAAGGGAACCGGAACCGCAAACCAGTGCCCCACCATTGAAGGGGGAGTGGAATCATTTTCCTTCAAGGCCGGGAAGTACAATGCCAAGAAGTTCTGCCTTGAACCCACTTCATTCACAGTGAAGGCAGAGGGAGTAGCCAAGAACGCCCCACTTGAGTTCCAAAACACCAAGCTCATGACACGTCTGACCTACACCCTCGACGAGATCGAAGGACCCTTTGAGGTTTCCTCTGATGGCACTGTCAAGTTCGAGGAGAAAGATGGCATTGACTACGCTGCTGTCACAGTTCAGCTTCCCGGTGGCGAGCGTGTTCCATTCCTTTTCACCATCAAACAGTTGGTAGCATCTGGGAAGCCAGACAGCTTCAGTGGGGAGTTTCTAGTGCCTTCATACCGTGGATCTTCCTTCTTGGACCCCAAGGGAAGAGGTGCGTCAACTGGTTATGACAATGCTGTCGCATTGCCTGCTGGTGGCAGAGGAGATGAGGAAGAACTTGCTAAGGAGAACAACCAGAGTGCTTCTTCATCCCAAGGGAAGATCACCTTGAGCGTGACACAGAGCAAGCCTGATACCGGTGAGGTGATTGGTGTGTTCGAGAGCATTCAGCCGTCCGACACTGATTTGGGAGCGAAAGCTCCCAAGGATGTGAAGATCCAGGGAGTTTGGTATGCTCAGCTCGAGTCATAGACAGCTTTATCTCTCTTCTGCTTTATTTTGTATTTTGTTGTAACTTCTCAGTGTTGCTGCCATTACCTTTGACACCACTGTCCCAGCATGAGAGTGTTATCCTTGTTTGTATGTATACTATCGACTTTCAATTATAATGCTCGAAAATGTCCAAGGTTT
+AGCAGTGTTCCCATGAAACCTTCCCACTGAGTCAACTCACTCTGTACATAAAACCCTCTTCATCATCATCATGGCTTCTCAAGTTTTTCTTCAGCAAGGGTTGTTACTGTTTGCCCCAAACCAATGTTCTCCAACCAAGCTCGGTGTATCTTCTTGCCTCGGTTCTCGTAACTTTCCGTTGATTTCCTCCACCTCAATTTCATGGCGTTGCAACAACCCTCTCTCTGCCAAACCCTCTTTTGTTGTCAGAGCTGACTCCAATGTCGACGCTGCTTCCGACAATGCTGGTGAAGTTCCAGAAGCTGAAGGTAGCGTTGATCAGGTTCCTGAAGATGGAGAAGCAGAACTAGCTTCGGATTCTGAGGTGGAGCAACCCAAGCCCCCTAGAAAGCAACGAGTCAAGCTTGGAGATGTTATGGGGATATTGAATCAGAGGGCAATTGAGGCATCGGAAAGCATGAGGCCGACTCCAGAAATTAGGACTGGAGATGTTGTGGAAATCAAACTGGAAGTTCCTGAGAACAAGCGTAGGTTGTCTATTTATAAAGGTATAGTCATCTCAAGACAAAATGCTGGTATTCACACAACTATTCGAATCCGAAGGATTATTGCTGGCACAGGGGTTGAGATTGTCTTCCCAATTTACTCACCAAACATCAAAGAAATCAAAGTGGTAAACCACCGTAAAGTCAGAAGAGCAAGATTGTACTATTTAAGAGACAAGCTTCCCAGATTCTCCACTTTCAAATGATACGGTTACCACTTCTCATCCTGATCTTCTTCAAAGTAGTTGCTGATATTGCAGGGCCATATTTTGGTTATTTCGTTTTGTTGTGTTGTAGAATATATCATTTTTCTTCCTCTAAATCTATCCTCCGAGAATTGGAAACAAGTGTATGTATGTTGCCCTTGATAATATTTGAAATTTGAAGTGTTCTCCCTTGCATTCCTTGGTATAGGATAGAAAGCCAAGCTCCTAAACAAACATTACTAAATATGACAGTCTAAGGAATGAGCATGTGTATCGATACCAGTTAAGTGCATTGTGAATGTATTTTTTTTTTTTATCTCTATCCATAAAAAAAGGTATGTTCATTCTTG
+AAGAAACAAGAGAGAGAAGATGATTTAGATGAGCCAAAAACAAAGGAAAAACGGCAAAAGGGAGAGAAAGGAAAATCTCCATCAGGTTTTCTTGCTCCTCTCCAGCTATCTGATGCCCTTGTAAACTTCCTTGGTACTGGAGAAAGTGAATTATCAAGATCTGATGTCATAAAAAGAATGTGGGAATACATAAAAGGAAACGACCTTCAGGATCCTTCTGACAAGAGGAAAATATTATGCGACGACAAGCTGAAAGAACTCTTTGATGTGGACTCCTTTAACGGCTTCACCGTTACAAAACTGTTGACTCCTCATTTTATAAAGGCAGAGCAGTGAGTTGCTTGTGGAAATCGGTAATGTTGTCCAATTAGGTTTGGAAGGTCCTTCTTTTGTGGCCTTTTGGCATTGTCTGCCAACACGAGGAATAGGAATTAGGAACATGACAGATTTTCAGTAAATTTTTCTCCAAGAATTTAATGTTACGTGACCATTACTTTGTTTTTTTTAATATCACGTTTTGTCACTTGGCAGTTGAAATTTTTGTATATTTTCAGTTCCTGAAGCTGCAAGGATAATGCTGACTTCTTACTCTACTCTGCATTTGCTCATATGAGGCACTACACATATCCATAATACATGAATAAATTTGCAGTATTGAA
+CATTTGTTCCATTTGCTCAGGCATTTGCAGCTGTACTTACAGCTGTCCTTACTGGTTCTCTCTATTATGTGGCTGCCTCTCCTAAAGATCCTACTTATATTGTGGCACCTGTTTTACAGTCTCGCTCTGGTCGTCAAGATTTGAAAAAGCTATTTGAAGCCTGGTATGAGAAACGGCAAATGAAAAAAATATATTCACCACTTCTGGAAGGACTACTAGCTCTCTACCTAGGATTTGAGTGGATCCAAACGAATAACATTCTTGCTCCCATTATCACACATGGCATATACTCCACAGTTATATTGGGACATGGCCTTTGGAAGATAAACGACCACCGGCGAAGACTACGTCAAAGAATCCAACAGCTCAAATCTGAAGAACAAAATTCCCAGTAGACTTTGAAATACCTTCCATGTCTGGCTGTGATACAAAAAATGTATATGTATGTATTAGAGCTGCTAATTATGTAAAGAGAAAAGATGTATATACTTGTGTTAGCTGAGGTCTCGTACACACTGAATATTCAGGTTTTGTTCACCATTTTCTAATTTCGAGTTACTATATGTAGTGTTTTCTAATAAAATGAAATAAAATCCCCAAGTTGGGTTGATTTAAATT
+GAGACCTGTTATGATTCACAGAGCCATTCTAGGATCTGTTGAGCGCATGTTTGCCATTCTTTTAGAGCACTACAAGGGTAAATGGCCCTTGTGGCTCAGTCCTCGTCAAGCAATTGTATGTCCTGTGTCAGAGAAATCACAAGCTTATGCACTGCAGGTGCGAGATCAGATCCACCAAGCAGGATATCACGTTGATGCTGATACAACTGATCGGAAGATTCAGAAGAAGGTACGGGAAGCTCAATTAGCGCAGTACAACTACATCTTGGTTGTTGGAGAGGAGGAAGCTAATACAGGACAGGTGAGTGTACGGGTTAGAGATAAAGCAGACCATAGCGTTATGAGTATTGAGAATCTACTCAAACACTTCAGCGACGAAGTTGCAGCTTTTCATTGATACTTCTCTTGTGAAAACTGTTGGAAGCAAATTTTACCCCCACTCACCTAGTTTGTTCACACTTTGTGTGCATTATTTATATTTTCAGCCTGACAATTTACATTTAGATGATTTGGGTAATGACTGTATTTTCTATGTGAATTTTGGAGCGCACTGATATCGATCCATTGTTTGAAAAGCTGAGAGAAAGTGTAATCTTTTATTTTCTGTCTACATTTTAATTATGTTTTTCGTTAGTTTTTTCCTTTTATATATTTGTTTGTTAAATTGAAGGAAACTATTGTTGG
+GGCACCAGGGATCTTACAAGGCTGGATCTCCATAATAACAAGTTGACAGGGCCTATTCCTCCTCAAATTGGACGGTTGAAGCGTCTTAAAATACTCAATTTGAGGTGGAACAAACTACAGGATGCAATTCCTCCAGAAATTGGCGAGCTTAAAAGTTTAACACATCTGTACCTAAGCTTCAATAGTTTCAAGGGAGAAATTCCCAAAGAGCTAGCAAATCTTCCAGACCTTCGCTACCTTTATCTTCATGAAAACCGTTTAATTGGTAGGATACCACCTGAGTTGGGCACTCTACAAAACCTTCGGCACTTGGATGCTGGTAACAATCATTTGGTGGGTACCATAAGGGAACTCATTCGTATTGAAGGTTGCTTTCCAGCACTCCGCAATCTATATCTAAACAATAATTATTTTACTGGAGGAATGCCTGCACAACTTGCCAACTTATCCAGTCTTGAGATCTTGTACCTGTCCTACAATAAAATGTCAGGAGTTATACCATCTAGCCTTGCTCATATTCCTAAATTGACATACTTGTACTTGGATCACAATCAGTTTTCGGGGAGAATTCCCGAACCCTTTTACAAACATTCATTTTTGAAAGAAATGTACATCGAGGGAAATGCATTCCGGCCTGGTGTTAAACCCATTGGTTTCCATAAAGTGCTTGAAGTTTCTGATTCAGACTTCCTTGTTTAATGAAACTCAACATATTTAGTTTTTTAGGAAGTTTACGTGTATAATTAATGAAACAATAGCTCCTCTGATTTTCTCAATGAAAATTGCTATATGGGTAATTCAATTTTTGTCACGGCTGTCTTGTCAGAAGAATCAATAAATAATAGTGTTTTTTAACTCT
+GGAAATGAGCACAATGTTAAGCAGATCAAGAATTACCGCCAAAAGGTTGAGGAGGAACTCTCCAAAATTTGTGGTGACATCCTGACTATTATAGACCAGCATCTAATTCCTTCTTCCGCCTCAGCAGAAGCTAGTGTTTTCTACTATAAGATGAAAGGTGATTATTATCGGTATCTTGCTGAGTTCAAGACCGACCAAGAAAGGAAAGAGGCAGCCGAGCAGTCACTCAAGGGATATGAGGCTGCTTCAGCCACTGCCAACACCGATCTTCCATCAACACATCCAATCCGTCTTGGACTTGCTCTCAACTTCTCTGTCTTTTATTACGAGATCATGAACTCTCCTGAAAGGGCCTGCCATTTGGCTAAACAAGCTTTTGATGAGGCAATTGCAGAGTTGGACACCTTGAGTGAAGAGTCATACAAGGACAGTACTTTGATCATGCAGTTGTTGAGAGACAACCTGACTCTCTGGACATCCGATTTGCCAGAAGATGGAGGCGAGGAGAACATAAAAGCTGAAGAAGCCAAACCTACTGAGCCTGAGAATTAACTAGGTTCTTTTGGATCTTTGGCCCTGATTCAATAGTCAGATTTTTGTGGTGCTCTGCAAAGAGGGCATTTTTCAGCTTTTCTTGCAATGGATTTGGAATGGACAATATGAGCTGTCGCCACTTCATAATTACCAACCAAAGCCAAAAGATCTGAGCCTGCCTTTTCTTTATTTCTTTAAATTGTTTTTCTTTCTTACTGCCTTTATCTATTTTAAGCAAAGTGGTCGGTTGAAACAATGGATAATTCACATTTAAATCATAAGAATCTTTTTCAAGTGTTCATTACATCCGTTTTGGTTCGTTTAAAATATTGTTTCCTATGCGCTCCTAGATGGGATACAGTACAAGTATTCAACTGTTGAGCAGAGATTTTTACCTCAAAAAATTAGT
+AGACACAACATCATAGAAACAGATCAACAACACATTAAAATTAGCATGGATCATAGCTTACGTTGTTTTGGGTCGACACTACCCAAAACTCTTCTTCAGTTTCTGTTATCACCTTCACTCCTTCTCTTCATCTCCTTCTTCAGTTTCTCCAACGCAGCCTTCGACCTCGCCACCATACCCTTCAACGATGCCTATTCACCCCTCTTTGGGGATGGCAACCTTGTCCGCTCCGCCGATGGCAACGGTGTTCAACTCCTCCTCGATCGCTTCACCGGTTCTGGTTTCGTTTCTTCCAATATGTACCAGCATGGATTCTTCAGCGCCAATATCAAGCTACCATCGAATTACAGCGCTGGTATTTGCGTGGCCTTTTATACATCAAACAATGAGATGTTTGAGAAGACACACGATGAGTTAGACTTTGAATTCTTAGGTAATATAGCCGGAAAGCCTTGGAGGTTTCAGACAAACTTGTACGGCAATGGCAGCACCAACCGTGGCCGTGAGGAGCGGTACCGCCTCTGGTTTGATCCAACCAAGGGATTCCATAGATACAGCATTCTATGGACAGCTAAGAACATCATATTTTACATAGATGAGGTTCCAATTAGAGAAATTATAAGAAGTGAAGAAATGGGAGCTGATTACCCAGCAAAGCCAATGGCATTATACGCCACAATATGGGATGCATCAAATTGGGCCACATCGGGTGGAAA

data/spec/data/prot_seqs_lower.txt

@@ -0,0 +1,3 @@
+>Lowercase_sequence
+meqywsgsainenkgmvenlqrygiiksskvaetmekidrglfvpngvqpyidspmsigynatisaphmhatclqllenylqpgmhaldvgsgtgyltacfammvgpngravgvehipelvsfsinnieksaaapqlkdgslsvhegdgrqgwpefatydaihvgaaapeipqplidqlktggrmiipvgnvfqdlkvvdknsdgsisirtetsvryvpltskeaqlke
+meqywsgsagiiksskvaetmekidrglfvpngvqpyidspmsigynatisaphmhatclqllenylqinenkgmvenlqrypgmhaldvgsgtgyltacfammvgpngravgvehipelvsfsinnieksaaapqlkdgslsvhegdgrqgwpefatydaihvgaaapeipgiiksskvaetmekidrglfvpngvqpyidspmsigynatisaphmhatclqllenylqplidqlktggrmiipvgnvfqdlkvvdknsdgsisirtetgiiksskvaetmekidrglfvpngvqpyidspmsigynatisaphmhatclqllenylqsvryvpltskeaqlke

data/spec/data/prot_seqs_mixed.txt

@@ -0,0 +1,3 @@
+>Mixed_case_sequence
+mEqywSGSAINeNkGmvEnLqRYgiIksskvAEtmekidrGlfVpnGvqpyIdSPMSIgyNATISapHMhAtcLqLLenyLqPGMHaLDVGsGTGYLtACFamMVgpNGrAvgVEHIPelVsFsiNniEksaAApqLkdGSlsvhEgdGRQgWPEfaTyDAiHvGaaaPeipQplidqLkTgGrmiipvgNVfqDlKVVdkNsdGSisirTETsVrYvpLTskEAqLKE
+MEQYwSGSaGIIkSSkVAEtmeKidRGLfVpNGVQpYiDspMsigyNaTisaPhmHAtCLqLlEnYlQineNKgMvEnlqRypGmHAlDVgsgtGYltACFamMVGPNGRaVgvehipElvSFSInNIekSaAapqlkdGSLsVhEGDgRqgwPeFATyDaiHvgaAAPeIPGiiksSkVAeTMEKidRglFVpNgvQpYiDspMsIGyNATisaPhmhATCLqLlENYLqplIdQLkTgGRMiipVGnVfqDlKvVDknSDgsISIrTeTgIIkSSKVaEtMEkidrGlFVpNgVQPYidsPmSiGyNaTiSapHmHAtcLqLlEnyLqSvRYvPLtSKeAQlKE

data/spec/data/{prot_seqs.txt → prot_seqs_upper.txt}

@@ -1,4 +1,3 @@
->ADA84676.1 protein L-isoaspartyl methyltransferase 1 [Cicer arietinum]
+>Uppercase_sequence
 MEQYWSGSAINENKGMVENLQRYGIIKSSKVAETMEKIDRGLFVPNGVQPYIDSPMSIGYNATISAPHMHATCLQLLENYLQPGMHALDVGSGTGYLTACFAMMVGPNGRAVGVEHIPELVSFSINNIEKSAAAPQLKDGSLSVHEGDGRQGWPEFATYDAIHVGAAAPEIPQPLIDQLKTGGRMIIPVGNVFQDLKVVDKNSDGSISIRTETSVRYVPLTSKEAQLKE
->ADA84676.2 protein L-isoaspartyl methyltransferase 1 [Cicer arietinum]
 MEQYWSGSAGIIKSSKVAETMEKIDRGLFVPNGVQPYIDSPMSIGYNATISAPHMHATCLQLLENYLQINENKGMVENLQRYPGMHALDVGSGTGYLTACFAMMVGPNGRAVGVEHIPELVSFSINNIEKSAAAPQLKDGSLSVHEGDGRQGWPEFATYDAIHVGAAAPEIPGIIKSSKVAETMEKIDRGLFVPNGVQPYIDSPMSIGYNATISAPHMHATCLQLLENYLQPLIDQLKTGGRMIIPVGNVFQDLKVVDKNSDGSISIRTETGIIKSSKVAETMEKIDRGLFVPNGVQPYIDSPMSIGYNATISAPHMHATCLQLLENYLQSVRYVPLTSKEAQLKE

data/spec/quorum/quorum_sequence_spec.rb

@@ -47,16 +47,44 @@ describe "Quorum::Sequence" do
   end
 
   describe "#discover_input_sequence_type" do
-    it "should return 'nucleic_acid' when fed nucleic acid sequences" do
+    it "should return 'nucleic_acid' when fed uppercase nucleic acid sequences" do
       sequence = File.open(
-        File.expand_path("../../data/nucl_seqs.txt", __FILE__)
+        File.expand_path("../../data/nucl_seqs_upper.txt", __FILE__)
       ).read
       discover_input_sequence_type(sequence).should eq("nucleic_acid")
     end
 
-    it "should return 'amino_acid' when fed amino acid sequences" do
+    it "should return 'nucleic_acid' when fed lowercase nucleic acid sequences" do
       sequence = File.open(
-        File.expand_path("../../data/prot_seqs.txt", __FILE__)
+        File.expand_path("../../data/nucl_seqs_lower.txt", __FILE__)
+      ).read
+      discover_input_sequence_type(sequence).should eq("nucleic_acid")
+    end
+
+    it "should return 'nucleic_acid' when fed mixed case nucleic acid sequences" do
+      sequence = File.open(
+        File.expand_path("../../data/nucl_seqs_mixed.txt", __FILE__)
+      ).read
+      discover_input_sequence_type(sequence).should eq("nucleic_acid")
+    end
+
+    it "should return 'amino_acid' when fed uppercase amino acid sequences" do
+      sequence = File.open(
+        File.expand_path("../../data/prot_seqs_upper.txt", __FILE__)
+      ).read
+      discover_input_sequence_type(sequence).should eq("amino_acid")
+    end
+
+    it "should return 'amino_acid' when fed lowercase amino acid sequences" do
+      sequence = File.open(
+        File.expand_path("../../data/prot_seqs_lower.txt", __FILE__)
+      ).read
+      discover_input_sequence_type(sequence).should eq("amino_acid")
+    end
+
+    it "should return 'amino_acid' when fed mixed case amino acid sequences" do
+      sequence = File.open(
+        File.expand_path("../../data/prot_seqs_mixed.txt", __FILE__)
       ).read
       discover_input_sequence_type(sequence).should eq("amino_acid")
     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: quorum
 version: !ruby/object:Gem::Version
-  version: 0.3.2
+  version: 0.3.3
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-06-22 00:00:00.000000000 Z
+date: 2012-07-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -323,7 +323,12 @@ files:
 - script/rails
 - spec/data/nucl_prot_seqs.txt
 - spec/data/nucl_seqs.txt
-- spec/data/prot_seqs.txt
+- spec/data/nucl_seqs_lower.txt
+- spec/data/nucl_seqs_mixed.txt
+- spec/data/nucl_seqs_upper.txt
+- spec/data/prot_seqs_lower.txt
+- spec/data/prot_seqs_mixed.txt
+- spec/data/prot_seqs_upper.txt
 - spec/data/seqs.docx
 - spec/data/seqs_not_fa.txt
 - spec/data/tmp/test.tgz
@@ -435,7 +440,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -642761823290379007
+      hash: -91775132015006220
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -444,7 +449,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -642761823290379007
+      hash: -91775132015006220
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.24