Updated tests.

app/Main.hs

@@ -14,7 +14,7 @@ import           Data.List
 import           Data.Maybe
 import           Data.String
 import           Prelude                    (error)
-import           System.Console.CmdArgs
+import           System.Console.CmdArgs.Implicit
 import           System.IO
 import           Table
 import           Text.Show
@@ -35,21 +35,26 @@ data UserInput = UserInput
 --note, to use a tab character, one needs to enter a literal tab on the command
 --line. Eg. delimiter="     "
 --do this via Ctrl-V<tab>
-userInput :: Mode (CmdArgs UserInput)
-userInput =  cmdArgsMode UserInput
+feht :: UserInput
+feht =  UserInput
     {info = def &= help "File of genome metadata information"
     ,one = "allbut" &= help "Name and list of meta values for group one"
     ,two = "allbut" &= help "Name and list of meta values for group two"
     ,datafile = def &= help "File of binary or snp data"
     ,mode = def &= help "mode of program, either 'binary', or 'snp' "
     ,delimiter = "\t" &= help "Delimiter used for info and data files"
     ,mtc = "Bonferroni" &= help "Multiple testing correction, 'bonferroni', 'none'"
-    }
+    } &=
+    program "feht" &=
+    summary "Predictive marker discovery for groups: binary data, genomic data (single nucleotide variants), and arbitrary character data." &=
+    details ["feht takes a table of character data, and a file of metadata, and produces markers that are predictive of groups", "", "    ./feht --info=data/metadata.txt --datafile=data/data.tab --mode='snp' > output.txt"]
+
 
 
 main :: IO ()
 main = do
-    userArgs <- cmdArgsRun userInput
+    userArgs <- cmdArgs feht
+    userArgs <- cmdArgs feht
     let onexs = words $ one userArgs
     let twoxs = words $ two userArgs
     let groupOneCategory = MetaCategory $ BS.pack $ head onexs
@@ -90,7 +95,6 @@ main = do
 
     let geneVectorMap = getGeneVectorMap delim finalGenomeData
     let cl = getComparisonList metadataTable (groupOneCategory, groupOneValues) (groupTwoCategory, groupTwoValues)
-    --print cl
 
     let compList = fmap (calculateFetFromComparison geneVectorMap) cl
 

feht.cabal

@@ -16,20 +16,20 @@ cabal-version:       >=1.10
 library
   hs-source-dirs:      src
   exposed-modules:     FET, Comparison, Table, StorableByteString
-  build-depends:       base >= 4.7 && < 5
+  build-depends:       base
                        , bytestring
                        , hashable
                        , unordered-containers
                        , vector
                        , statistics
-                       , time
                        , safe
+                       , QuickCheck
   default-language:    Haskell2010
 
 executable feht
   hs-source-dirs:      app
   main-is:             Main.hs
-  ghc-options:         -threaded -rtsopts -with-rtsopts=-N -O2 -static -optl-static -optl-pthread
+  ghc-options:         -threaded -optl-pthread -optl-static -fPIC -optc-Os
   build-depends:       base
                      , bytestring
                      , cmdargs
@@ -46,6 +46,7 @@ test-suite feht-test
                      , QuickCheck
                      , feht
                      , bytestring
+                     , ieee754
   ghc-options:         -threaded -rtsopts -with-rtsopts=-N
   default-language:    Haskell2010
 

src/Table.hs

@@ -18,7 +18,6 @@ import           Data.List                  (zip, (++))
 import           Data.Maybe
 import           Data.Ord
 import           Data.String
-import qualified Data.Time.Calendar         as C
 import qualified Data.Vector.Unboxed        as V
 import           GHC.Generics               (Generic)
 import           Prelude                    (Integer, error, undefined, (+))

stack.yaml

@@ -1,11 +1,10 @@
 # For more information, see: https://github.com/commercialhaskell/stack/blob/release/doc/yaml_configuration.md
 
 # Specifies the GHC version and set of packages available (e.g., lts-3.5, nightly-2015-09-21, ghc-7.10.2)
-resolver: lts-6.5
+resolver: lts-7.13
 
 # Local packages, usually specified by relative directory name
 packages:
-- '.'
 
 # Packages to be pulled from upstream that are not in the resolver (e.g., acme-missiles-0.3)
 extra-deps: []

test/Spec.hs

@@ -1,7 +1,91 @@
+{-# LANGUAGE OverloadedStrings          #-}
+
+module Main where
+
 import Test.Hspec
 import Test.QuickCheck
 import Control.Exception (evaluate)
-import FETSpec
+import FET
+import qualified Data.ByteString.Lazy.Char8 as BS
+import Data.AEq
+import Numeric.IEEE
+
+
+main :: IO ()
+main = hspec $
+    describe "Verify p-values of FET tests" $ do
+        it "matrix of 2 7 5 3 two tail" $ do
+            let fr = fet (FETName "two tail test")
+                         (GroupOneA 2)
+                         (GroupOneB 7)
+                         (GroupTwoA 5)
+                         (GroupTwoB 3)
+                         TwoTail
+            let aeq = pvalue fr ~== (0.153434800493624::Double)
+            aeq `shouldBe` True
+        it "matrix of 2 7 5 3 one tail" $ do
+            let fr = fet (FETName "one tail test")
+                         (GroupOneA 2)
+                         (GroupOneB 7)
+                         (GroupTwoA 5)
+                         (GroupTwoB 3)
+                         OneTail
+            let aeq = pvalue fr ~== (0.11703002879473468::Double)
+            aeq `shouldBe` True
+        it "matrix of 129 173 152 138 two tail" $ do
+            let fr = fet (FETName "two tail")
+                         (GroupOneA 129)
+                         (GroupOneB 173)
+                         (GroupTwoA 152)
+                         (GroupTwoB 138)
+                         TwoTail
+            let aeq = pvalue fr ~== (2.1126884355092402e-2::Double)
+            aeq `shouldBe` True
+        it "matrix of 129 173 152 138 one tail" $ do
+            let fr = fet (FETName "one tail")
+                         (GroupOneA 129)
+                         (GroupOneB 173)
+                         (GroupTwoA 152)
+                         (GroupTwoB 138)
+                         OneTail
+            let aeq = pvalue fr ~== (1.1267280239712145e-2::Double)
+            aeq `shouldBe` True
+        it "matrix of 222 211 444 555 two tail (ChiSquared)" $ do
+            let fr = fet (FETName "two tail Chi Squared")
+                         (GroupOneA 222)
+                         (GroupOneB 211)
+                         (GroupTwoA 444)
+                         (GroupTwoB 555)
+                         TwoTail
+            let aeq = pvalue fr ~== (1.7384585693541843e-2::Double)
+            aeq `shouldBe` True
+        it "matrix of 222 211 444 555 one tail (ChiSquared)" $ do
+            let fr = fet (FETName "one tail ChiSquared")
+                         (GroupOneA 222)
+                         (GroupOneB 211)
+                         (GroupTwoA 444)
+                         (GroupTwoB 555)
+                         OneTail
+            let aeq = pvalue fr ~== (8.692292846770922e-3::Double)
+            aeq `shouldBe` True
+        it "matrix of 99222 98211 77444 74555 two tail (ChiSquared)" $ do
+            let fr = fet (FETName "two tail Chi-Squared")
+                         (GroupOneA 99222)
+                         (GroupOneB 98211)
+                         (GroupTwoA 77444)
+                         (GroupTwoB 74555)
+                         TwoTail
+            let aeq = pvalue fr ~== (4.7092508444146475e-5::Double)
+            aeq `shouldBe` True
+        it "matrix of 100998 100555 501 555 one tail (ChiSquared)" $ do
+            let fr = fet (FETName "one tail Chi-Squared")
+                         (GroupOneA 100998)
+                         (GroupOneB 100555)
+                         (GroupTwoA 501)
+                         (GroupTwoB 555)
+                         OneTail
+            let aeq = pvalue fr ~== (4.193675848378964e-2::Double)
+            aeq `shouldBe` True