diff --git a/LICENSE b/LICENSE
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--- /dev/null
+++ b/LICENSE
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+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
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+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ {one line to give the program's name and a brief idea of what it does.}
+ Copyright (C) {year} {name of author}
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see .
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ {project} Copyright (C) {year} {fullname}
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+.
diff --git a/Setup.hs b/Setup.hs
new file mode 100644
--- /dev/null
+++ b/Setup.hs
@@ -0,0 +1,2 @@
+import Distribution.Simple
+main = defaultMain
diff --git a/app/Main.hs b/app/Main.hs
new file mode 100644
--- /dev/null
+++ b/app/Main.hs
@@ -0,0 +1,571 @@
+{- heatitup
+Gregory W. Schwartz
+
+Find duplications a sequence.
+-}
+
+{-# LANGUAGE BangPatterns #-}
+{-# LANGUAGE OverloadedStrings #-}
+{-# LANGUAGE PartialTypeSignatures #-}
+{-# OPTIONS_GHC -fno-warn-partial-type-signatures #-}
+
+module Main where
+
+-- Standard
+import Control.Monad
+import Data.Char
+import Data.Maybe
+import Data.Bool
+import Data.Semigroup ((<>))
+import qualified Data.Map.Strict as Map
+import qualified Data.Set as Set
+import qualified System.IO as IO
+
+-- Cabal
+import Control.Lens
+import Data.Colour.SRGB (sRGB24read)
+import Data.Fasta.ByteString
+import Diagrams.TwoD.Size (mkWidth, mkHeight)
+import Options.Applicative
+import Pipes
+import Pipes.Csv
+import Safe
+import Diagrams.TwoD.Size
+import Diagrams.Backend.PGF (renderPGF, PGF)
+import Diagrams.Backend.SVG (renderSVG, SVG)
+import Diagrams.Backend.Html5 (renderHtml5, Html5)
+import Diagrams.Backend.Rasterific (renderRasterific, Rasterific)
+import qualified Diagrams.Prelude as D
+import qualified Data.ByteString.Char8 as C
+import qualified Data.Vector as V
+import qualified Pipes.ByteString as PB
+import qualified Pipes.Prelude as P
+
+-- Local
+import Types
+import Utility
+import Load
+import Repeated
+import Spacer
+import Classify
+import Plot
+import Print
+
+-- | Command line arguments
+data Options = Options { input :: Maybe String
+ , spacerFlag :: Bool
+ , refInput :: Maybe String
+ , blacklistInput :: Maybe String
+ , output :: Maybe String
+ , outputPlot :: Maybe String
+ , outputSize :: Double
+ , outputLabel :: String
+ , refField :: Int
+ , posField :: Maybe Int
+ , ignoreField :: Maybe Int
+ , inputMinSize :: Int
+ , gaussWindow :: Int
+ , gaussTime :: Double
+ , gaussThreshold :: Double
+ , inputMinMut :: Maybe Int
+ , inputDistance :: Int
+ , refCheckBlacklistFlag :: Bool
+ , refRecBlacklistFlag :: Bool
+ , minRichness :: Int
+ , inputColorDupL :: String
+ , inputColorDupR :: String
+ , inputColorMut :: String
+ , inputColorSpacer :: String
+ , inputColorBackground :: String
+ , inputColorForeground :: String
+ }
+
+-- | Command line options
+options :: Parser Options
+options = Options
+ <$> optional ( strOption
+ ( long "input"
+ <> short 'i'
+ <> metavar "FILE"
+ <> help "The input file"
+ )
+ )
+ <*> switch
+ ( long "spacer"
+ <> short 's'
+ <> help "Whether to characterize the spacer. Requires\
+ \ reference-input and matching labels for the input and\
+ \ reference-input to compare."
+ )
+ <*> optional ( strOption
+ ( long "reference-input"
+ <> short 'I'
+ <> metavar "[Nothing] | FILE"
+ <> help "The input file containing the reference sequences to compare\
+ \ to. The first entry in the field must be the accession and\
+ \ match the requested field from reference-field for the\
+ \ input. With no supplied file, no spacer will be annotated."
+ )
+ )
+ <*> optional ( strOption
+ ( long "blacklist-input"
+ <> short 'b'
+ <> metavar "[Nothing] | FILE"
+ <> help "The input fasta file containing possible false positives --\
+ \ sequences which may be duplicate nucleotides in the\
+ \ reference sequence."
+ )
+ )
+ <*> optional ( strOption
+ ( long "output"
+ <> short 'o'
+ <> metavar "FILE"
+ <> help "The output file"
+ )
+ )
+ <*> optional ( strOption
+ ( long "output-plot"
+ <> short 'O'
+ <> metavar "FILE"
+ <> help "The output file for the plot. Each new plot gets a new number\
+ \ on it: output_1.svg, output_2.svg, etc. Each plot uses the\
+ \ first entry in the fasta header as the label. If FILE is\
+ \ HEADER (i.e. HEADER.pdf), uses the first entry in the fasta\
+ \ header as FILE along with the number. Supports html, png,\
+ \ tif, jpg, bmp, svg, and pdf. svg may render text differently\
+ \ in different situations, and pdf uses LaTeX for rendering\
+ \ and may also have issues if reads are too long, but the\
+ \ options are there and may be fixed in future releases."
+ )
+ )
+ <*> option auto
+ ( long "output-size"
+ <> short 'u'
+ <> metavar "SIZE"
+ <> value 20
+ <> help "([20] | DOUBLE) The size of the sequence image output."
+ )
+ <*> strOption
+ ( long "label"
+ <> short 'l'
+ <> metavar "STRING"
+ <> value ""
+ <> help "The label to use in the label column for the output"
+ )
+ <*> option auto
+ ( long "reference-field"
+ <> short 'f'
+ <> metavar "[1] | INT"
+ <> value 1
+ <> help "The field in each input header that contains the reference\
+ \ accession number to compare to. Results in an out of bounds\
+ \ if this field does not exist."
+ )
+ <*> optional ( option auto
+ ( long "position-field"
+ <> short 'p'
+ <> metavar "[Nothing] | INT"
+ <> help "The field in each input header that contains the starting\
+ \ position of the read. Added to the annotations. Results\
+ \ in out of bounds if this field does not exist."
+ )
+ )
+ <*> optional ( option auto
+ ( long "ignore-field"
+ <> short 'g'
+ <> metavar "[Nothing] | INT"
+ <> help "The field in each input header that contains a 0 or a 1:\
+ \ 0 means to ignore this read (assign as Normal) and 1\
+ \ means to find a duplication in this read.\
+ \ Used for reads where there is known to be no duplication\
+ \ and thus helps remove false positives."
+ )
+ )
+ <*> option auto
+ ( long "min-size"
+ <> short 'S'
+ <> metavar "[15] | INT"
+ <> value 15
+ <> help "The minimum size of a duplication"
+ )
+ <*> option auto
+ ( long "gaussian-window"
+ <> short 'w'
+ <> metavar "[3] | Double"
+ <> value 3
+ <> help "The window for the discrete gaussian kernel atypical spacer\
+ \ determination"
+ )
+ <*> option auto
+ ( long "gaussian-time"
+ <> short 't'
+ <> metavar "[2] | Double"
+ <> value 2
+ <> help "The time for the discrete gaussian kernel atypical spacer\
+ \ determination"
+ )
+ <*> option auto
+ ( long "gaussian-threshold"
+ <> short 'T'
+ <> metavar "[0.4] | Double"
+ <> value 0.4
+ <> help "The cutoff to be considered a mutation for the discrete\
+ \ gaussian kernel atypical spacer determination"
+ )
+ <*> optional ( option auto
+ ( long "min-mutations"
+ <> short 'm'
+ <> metavar "INT"
+ <> help "The minimum number of nucleotides between mutations"
+ )
+ )
+ <*> option auto
+ ( long "levenshtein-distance"
+ <> short 'L'
+ <> metavar "[2] | INT"
+ <> value 2
+ <> help "The minimum Levenshtein distance to the false positive\
+ \ checker. If the distance to the false positive string\
+ \ is less than or equal to this number,\
+ \ the duplication is considered\
+ \ a false positive. Compares candidates against each sequence\
+ \ in --blacklist-input"
+ )
+ <*> switch
+ ( long "reference-check-blacklist"
+ <> short 'c'
+ <> help "Whether to use the reference as a blacklist in addition to\
+ \ the supplied blacklist. That is, we check if the duplication\
+ \ can be found twice or more in the reference input."
+ )
+ <*> switch
+ ( long "reference-recursive-blacklist"
+ <> short 'r'
+ <> help "Whether to use the reference as a recursive\
+ \ blacklist in addition to\
+ \ the supplied blacklist. That is, the reference sequences\
+ \ are inputed with the same parameters (except distance, which\
+ \ here is 0)\
+ \ to the duplication finder, and those duplications found are\
+ \ added to the blacklist. This process is recursive, executed\
+ \ until no more duplications are found in the reference.\
+ \ Beware, too many blacklist entries can slow down the finder\
+ \ significantly, as each blacklist entry is compared with each\
+ \ candidate."
+ )
+ <*> option auto
+ ( long "min-richness"
+ <> short 'R'
+ <> metavar "[1] | INT"
+ <> value 1
+ <> help "The minimum nucleotide richness (number of different types of\
+ \ nucleotides) allowed in the duplication to be considered\
+ \ real. Useful if the user knows that a sequence like\
+ \ \"TTTTTTTTCTTTTTTTTC\" is not likely to be real."
+ )
+ <*> strOption
+ ( long "color-left-duplication"
+ <> metavar "[#a6cae3] | COLOR"
+ <> help "The color of the left side of the repeated sequence."
+ <> value "#a6cae3"
+ )
+ <*> strOption
+ ( long "color-right-duplication"
+ <> metavar "[#b0de8a] | COLOR"
+ <> help "The color of the right side of the repeated sequence."
+ <> value "#b0de8a"
+ )
+ <*> strOption
+ ( long "color-difference"
+ <> metavar "[#1978b3] | COLOR"
+ <> help "The color of discrepancies between the left and right side of\
+ \ the duplication."
+ <> value "#1978b3"
+ )
+ <*> strOption
+ ( long "color-spacer"
+ <> metavar "[#fdbd6e] | COLOR"
+ <> help "The color of the exogenous nucleotides within the spacer."
+ <> value "#fdbd6e"
+ )
+ <*> strOption
+ ( long "color-background"
+ <> metavar "[#ffffff] | COLOR"
+ <> help "The color of the background."
+ <> value "#ffffff"
+ )
+ <*> strOption
+ ( long "color-foreground"
+ <> metavar "[#000000] | COLOR"
+ <> help "The color of the foreground."
+ <> value "#000000"
+ )
+
+plotITDM :: Options
+ -> Colors
+ -> (Int, (ITD, FastaSequence))
+ -> IO (ITD, FastaSequence)
+plotITDM opts colors (!count, (!itd, !fs)) = do
+ let fileType = fmap ( fmap toLower
+ . reverse
+ . takeWhile (/= '.')
+ . reverse
+ )
+ . outputPlot
+ $ opts
+ firstField =
+ maybe
+ "output"
+ (fmap (\x -> if x == '.' || x == '/' then '_' else x) . C.unpack)
+ . headMay
+ . C.split '|'
+ . fastaHeader
+ $ fs
+ savefile = (++ "_" ++ show count ++ "." ++ fromJust fileType)
+ . (\x -> case reverse . drop 1 . dropWhile (/= '.') . reverse $ x of
+ "HEADER" -> firstField
+ y -> y
+ )
+ . fromJust
+ . outputPlot
+ $ opts
+ size = outputSize opts
+
+ case fileType of
+ (Just "pdf") -> renderPGF savefile (mkHeight size)
+ . (\x -> plotITD colors fs itd x :: D.Diagram PGF)
+ . Query
+ . fastaSeq
+ $ fs
+ (Just "svg") -> renderSVG savefile (mkHeight size)
+ . (\x -> plotITD colors fs itd x :: D.Diagram SVG)
+ . Query
+ . fastaSeq
+ $ fs
+ (Just "html") -> renderHtml5 savefile (mkHeight size)
+ . (\x -> plotITD colors fs itd x :: D.Diagram Html5)
+ . Query
+ . fastaSeq
+ $ fs
+ (Just "png") -> renderRasterific savefile (mkHeight size)
+ . (\x -> plotITD colors fs itd x :: D.Diagram Rasterific)
+ . Query
+ . fastaSeq
+ $ fs
+ (Just "tif") -> renderRasterific savefile (mkHeight size)
+ . (\x -> plotITD colors fs itd x :: D.Diagram Rasterific)
+ . Query
+ . fastaSeq
+ $ fs
+ (Just "jpg") -> renderRasterific savefile (mkHeight size)
+ . (\x -> plotITD colors fs itd x :: D.Diagram Rasterific)
+ . Query
+ . fastaSeq
+ $ fs
+ (Just "bmp") -> renderRasterific savefile (mkHeight size)
+ . (\x -> plotITD colors fs itd x :: D.Diagram Rasterific)
+ . Query
+ . fastaSeq
+ $ fs
+ (Just x) -> error $ x <> " filetype not supported for output."
+ Nothing -> return ()
+
+ return (itd, fs)
+
+getReferenceSeq :: Int -> FastaSequence -> ReferenceMap -> ReferenceSeq
+getReferenceSeq field fs = ReferenceSeq
+ . fastaSeq
+ . fromMaybe ( error
+ . (++) "Reference accession field not found in: "
+ . C.unpack
+ . fastaHeader
+ $ fs
+ )
+ . Map.lookup ( Accession
+ . getField field '|'
+ $ fs
+ )
+ . unReferenceMap
+
+-- | Unpack a longest substring into a string.
+unpackSubstring :: LongestSubstring -> String
+unpackSubstring = C.unpack . unSubstring . _dupSubstring . unLongestSubstring
+
+-- | Get a blacklist using a recursive method on the reference sequences. That
+-- is, repeatedly exhaust all possibly repeats in the reference sequences.
+-- Slower than the reference check if there are lots of sequences in the
+-- reference.
+refRecBlacklist :: RepeatConfig -> [FastaSequence] -> Blacklist
+refRecBlacklist !tempConfig fss =
+ case catMaybes longestList of
+ [] -> _blacklist tempConfig
+ xs -> refRecBlacklist
+ ( over blacklist ( Blacklist
+ . Set.union ( Set.fromList
+ . fmap unpackSubstring
+ $ xs
+ )
+ . unBlacklist
+ ) tempConfig
+ )
+ . catMaybes
+ . zipMaybe longestList
+ $ fss
+ where
+ longestList = fmap
+ ( longestRepeatedSubstringMutations tempConfig []
+ . Query
+ . fastaSeq
+ )
+ fss
+
+mainFunc :: Options -> IO ()
+mainFunc opts = do
+ hIn <- case input opts of
+ Nothing -> return IO.stdin
+ (Just x) -> IO.openFile x IO.ReadMode
+ hOut <- case output opts of
+ Nothing -> return IO.stdout
+ (Just x) -> IO.openFile x IO.WriteMode
+
+ refMap <- case refInput opts of
+ Nothing -> return Nothing
+ (Just x) -> IO.withFile x IO.ReadMode $ \hRefIn ->
+ fmap (Just . toReferenceMap (Field 1))
+ . readFasta
+ $ hRefIn
+
+ suppliedBlacklist <-
+ case blacklistInput opts of
+ Nothing -> return . Blacklist $ Set.empty
+ (Just x) -> IO.withFile x IO.ReadMode $ \hRefIn ->
+ fmap (Blacklist . Set.fromList . fmap (C.unpack . fastaSeq))
+ . readFasta
+ $ hRefIn
+
+ let colors = Colors { _colorDupL = sRGB24read . inputColorDupL $ opts
+ , _colorDupR = sRGB24read . inputColorDupR $ opts
+ , _colorMut = sRGB24read . inputColorMut $ opts
+ , _colorSpacer =
+ sRGB24read . inputColorSpacer $ opts
+ , _colorBackground =
+ sRGB24read . inputColorBackground $ opts
+ , _colorForeground =
+ sRGB24read . inputColorForeground $ opts
+ }
+ tempConfig = RepeatConfig
+ { _blacklist = suppliedBlacklist
+ , _refMap = refMap
+ , _richness = Richness . minRichness $ opts
+ , _distance = Distance 0
+ , _alphabet = "ATCG"
+ , _minSize = MinSize . inputMinSize $ opts
+ , _minMut = fmap MinMut . inputMinMut $ opts
+ , _refCheckFlag = refCheckBlacklistFlag opts
+ }
+ finalBlacklist =
+ if refRecBlacklistFlag opts
+ then refRecBlacklist tempConfig
+ . Map.elems
+ . unReferenceMap
+ . fromMaybe (error "No reference supplied.")
+ $ refMap
+ else suppliedBlacklist
+ config = set distance (Distance . inputDistance $ opts)
+ . set blacklist finalBlacklist
+ $ tempConfig
+ getDup fs = ( join
+ . fmap ( longestRepeatedSubstringMutations config []
+ . Query
+ . fastaSeq
+ )
+ . maybe (Just fs) (flip ignore fs)
+ . ignoreField
+ $ opts
+ , fs
+ )
+ getSpace Nothing (!dup, !fs) =
+ ( ITD { _duplication = fmap unLongestSubstring dup
+ , _spacer = Nothing
+ }
+ , fs
+ )
+ getSpace (Just rMap) (!dup, !fs) =
+ ( ITD { _duplication = fmap unLongestSubstring dup
+ , _spacer =
+ join
+ . fmap ( flip ( getSpacer
+ (Window $ gaussWindow opts)
+ (Time $ gaussTime opts)
+ (Threshold $ gaussThreshold opts)
+ refSeq
+ )
+ (Query . fastaSeq $ fs)
+ . unLongestSubstring
+ )
+ $ dup
+ }
+ , fs
+ )
+ where
+ refSeq = getReferenceSeq (refField opts) fs rMap
+ getClass (!itd, !fs) = (classifyITD itd, itd, fs)
+ addPos fs =
+ maybe (Position 1) (\ x -> Position
+ . read
+ . C.unpack
+ . fromMaybe ( error
+ $ "Position field out of bounds (use another field number): "
+ <> (C.unpack . fastaHeader $ fs)
+ )
+ . (flip atMay (x - 1))
+ . C.split '|'
+ . fastaHeader $ fs
+ )
+ . posField
+ $ opts
+ printRow (!c, !itd, !fs) =
+ printITD
+ (Label . C.pack . outputLabel $ opts)
+ (addPos fs)
+ fs
+ c
+ itd
+ headerOrder = V.fromList [ C.pack "label"
+ , C.pack "fHeader"
+ , C.pack "fSequence"
+ , C.pack "dSubstring"
+ , C.pack "dLocations"
+ , C.pack "dMutations"
+ , C.pack "sSubstring"
+ , C.pack "sLocation"
+ , C.pack "sOtherLocations"
+ , C.pack "classification"
+ ]
+
+ runEffect $ ( ( P.zip (Pipes.each [1..])
+ ( pipesFasta (PB.fromHandle hIn)
+ >-> P.map ( getSpace ( bool Nothing refMap
+ $ spacerFlag opts
+ )
+ . getDup
+ )
+ )
+ )
+ >-> P.mapM (plotITDM opts colors)
+ >-> P.map (printRow . getClass)
+ >-> encodeByName headerOrder
+ )
+ >-> PB.toHandle hOut
+
+ -- Finish up by closing file if written
+ unless (null . input $ opts) (IO.hClose hIn)
+ unless (null . output $ opts) (IO.hClose hOut)
+
+main :: IO ()
+main = execParser opts >>= mainFunc
+ where
+ opts = info (helper <*> options)
+ ( fullDesc
+ <> progDesc "Finds duplications in a sequence"
+ <> header "heatitup, Gregory W. Schwartz" )
diff --git a/heatitup.cabal b/heatitup.cabal
new file mode 100644
--- /dev/null
+++ b/heatitup.cabal
@@ -0,0 +1,75 @@
+name: heatitup
+version: 0.5.3.3
+synopsis: Find and annotate ITDs.
+description: Find and annotate ITDs using suffix trees and characterize the exogenous segments within the spacer using heat diffusion.
+homepage: http://github.com/GregorySchwartz/heatitup#readme
+license: GPL-3
+license-file: LICENSE
+author: Gregory W. Schwartz
+maintainer: gsch@pennmedicine.upenn.edu
+copyright: 2018 Gregory W. Schwartz
+category: Bioinformatics
+build-type: Simple
+-- extra-source-files:
+cabal-version: >=1.10
+
+library
+ hs-source-dirs: src
+ exposed-modules: Types
+ , Utility
+ , Load
+ , Repeated
+ , Diffusion
+ , Spacer
+ , Classify
+ , Plot
+ , Print
+ build-depends: base >= 4.7 && < 5
+ , bytestring
+ , bytestring-show
+ , cassava
+ , colour
+ , containers
+ , diagrams-lib
+ , edit-distance
+ , fasta
+ , lens
+ , pipes
+ , pipes-bytestring
+ , pipes-csv
+ , safe
+ , string-similarity
+ , stringsearch
+ , suffixtree
+ , vector
+ ghc-options: -O2
+ default-language: Haskell2010
+
+executable heatitup
+ hs-source-dirs: app
+ main-is: Main.hs
+ ghc-options: -threaded -rtsopts -O2
+ build-depends: base
+ , heatitup
+ , bytestring
+ , colour
+ , containers
+ , diagrams-core
+ , diagrams-lib
+ , diagrams-pgf
+ , diagrams-svg
+ , diagrams-html5
+ , diagrams-rasterific
+ , fasta
+ , lens
+ , optparse-applicative
+ , pipes
+ , pipes-bytestring
+ , pipes-csv
+ , safe
+ , vector
+ default-language: Haskell2010
+
+source-repository head
+ type: git
+ location: https://github.com/githubuser/heatitup
diff --git a/src/Classify.hs b/src/Classify.hs
new file mode 100644
--- /dev/null
+++ b/src/Classify.hs
@@ -0,0 +1,23 @@
+{- Classify
+Gregory W. Schwartz
+
+Classify an ITD.
+-}
+
+module Classify
+ ( classifyITD
+ ) where
+
+-- Standard
+
+-- Cabal
+
+-- Local
+import Types
+
+-- | Classify an ITD
+classifyITD :: ITD -> Classification
+classifyITD (ITD { _duplication = Nothing }) = Normal
+classifyITD (ITD { _spacer = Nothing}) = Typical
+classifyITD (ITD { _spacer = (Just s)}) =
+ if not . null . _spacerOtherLocations $ s then Atypical else Typical
diff --git a/src/Diffusion.hs b/src/Diffusion.hs
new file mode 100644
--- /dev/null
+++ b/src/Diffusion.hs
@@ -0,0 +1,48 @@
+{- Diffusion
+Gregory W. Schwartz
+
+Collections the functions pertaining to the discrete general diffusion
+equation, or the discrete Gaussian kernel
+-}
+
+{-# LANGUAGE BangPatterns #-}
+
+module Diffusion
+ ( diffuse
+ , mutationSignal
+ ) where
+
+-- Standard
+import Data.Maybe
+
+-- Cabal
+import qualified Data.Vector as V
+import qualified Data.ByteString.Char8 as C
+
+-- Local
+import Types
+import Utility
+
+-- | Diffuse a 1 dimensional discrete signal
+diffuse :: Window -> Time -> Signal -> Signal
+diffuse _ _ (Signal []) = Signal []
+diffuse (Window w) (Time t) (Signal xs) = Signal . V.toList . V.imap go $ vec
+ where
+ vec = V.fromList xs
+ go i x =
+ sum
+ . map ( \n -> (* g (fromIntegral n))
+ . fromMaybe 0
+ . (V.!?) vec
+ . fromIntegral
+ $ i - n
+ )
+ $ [(- w) .. w]
+ g n = (1 / (sqrt (2 * pi * t))) * (exp ((- n ^ 2) / (2 * t)))
+
+-- | Convert a hamming comparison to a signal
+mutationSignal :: C.ByteString -> Substring -> Signal
+mutationSignal base = Signal
+ . fmap (\x -> if x then 0 else 1)
+ . hammingList base
+ . unSubstring
diff --git a/src/Load.hs b/src/Load.hs
new file mode 100644
--- /dev/null
+++ b/src/Load.hs
@@ -0,0 +1,35 @@
+{- Print
+Gregory W. Schwartz
+
+Collections the functions pertaining to the loading of fasta files.
+-}
+
+module Load
+ ( readFasta
+ , toReferenceMap
+ ) where
+
+-- Standard
+import qualified Data.Map.Strict as Map
+import qualified System.IO as IO
+
+-- Cabal
+import Pipes
+import qualified Pipes.Prelude as P
+import qualified Pipes.ByteString as PB
+import Data.Fasta.ByteString
+
+-- Local
+import Types
+
+-- | Load an input fasta file.
+readFasta :: IO.Handle -> IO [FastaSequence]
+readFasta hRefIn =
+ runEffect $ P.toListM . pipesFasta . PB.fromHandle $ hRefIn
+
+-- | Convert a list of reference sequences to a map of their accessions
+toReferenceMap :: Field -> [FastaSequence] -> ReferenceMap
+toReferenceMap (Field x) =
+ ReferenceMap
+ . Map.unions
+ . fmap (\fs -> Map.singleton (Accession . getField x '|' $ fs) fs)
diff --git a/src/Plot.hs b/src/Plot.hs
new file mode 100644
--- /dev/null
+++ b/src/Plot.hs
@@ -0,0 +1,111 @@
+{- Plot
+Gregory W. Schwartz
+
+Collections the functions pertaining to plotting the sequence.
+-}
+
+{-# LANGUAGE BangPatterns #-}
+{-# LANGUAGE NoMonomorphismRestriction #-}
+{-# LANGUAGE FlexibleContexts #-}
+{-# LANGUAGE GADTs #-}
+{-# LANGUAGE PartialTypeSignatures #-}
+{-# OPTIONS_GHC -fno-warn-partial-type-signatures #-}
+
+module Plot
+ ( plotITD
+ ) where
+
+-- Standard
+import Data.Maybe
+import Data.List
+
+-- Cabal
+import qualified Data.ByteString.Char8 as C
+import Data.Colour.SRGB (sRGB24read)
+import Diagrams.Prelude
+import Data.Fasta.ByteString
+
+-- Local
+import Types
+
+foreground colors p (!xs, !ys)
+ | p `elem` xs = square 1 # fc (_colorMut colors) # lc (_colorMut colors)
+ | p `elem` ys = square 1 # fc (_colorSpacer colors) # lc (_colorSpacer colors)
+ | otherwise = mempty
+
+background colors p (!xs, !ys)
+ | p `elem` xs = _colorDupL colors
+ | p `elem` ys = _colorDupR colors
+ | otherwise = _colorBackground colors
+
+plotNucleotide colors nuc mut backG =
+ text nuc # fc (_colorForeground colors)
+ <> mut
+ <> square 1 # fc backG # lc backG
+
+plotITD
+ :: _
+ => Colors -> FastaSequence -> ITD -> Types.Query -> QDiagram b V2 n Any
+plotITD colors fs itd = hcat
+ . (:) ( text label
+ <> rect (genericLength label) 1 # lw none
+ )
+ . fmap (uncurry plotNuc)
+ . zip (fmap Position [0..])
+ . C.unpack
+ . unQuery
+ where
+ label = takeWhile (/= '|') . C.unpack . fastaHeader $ fs
+ dupLen = fromMaybe 0
+ . fmap (C.length . unSubstring . _dupSubstring)
+ . _duplication
+ $ itd
+ plotNuc p x =
+ plotNucleotide
+ colors
+ (x : [])
+ ( foreground colors p ( ( fromMaybe []
+ . fmap _dupMutations
+ . _duplication
+ $ itd
+ )
+ , ( fromMaybe []
+ . fmap _spacerOtherLocations
+ . _spacer
+ $ itd
+ )
+ )
+ )
+ ( background
+ colors
+ p
+ ( fromMaybe ([], [])
+ . fmap ( (\[x, y] -> (dupPositions x, dupPositions y))
+ . _dupLocations
+ )
+ . _duplication
+ $ itd
+ )
+ )
+ dupPositions (Position x) = fmap Position [x .. x + dupLen - 1]
+
+gruvColors :: String -> Colour Double
+gruvColors "background" = sRGB24read "#282828"
+gruvColors "foreground" = sRGB24read "#ebdbb2"
+gruvColors "black" = sRGB24read "#282828"
+gruvColors "darkgrey" = sRGB24read "#928374"
+gruvColors "darkred" = sRGB24read "#cc241d"
+gruvColors "red" = sRGB24read "#fb4934"
+gruvColors "darkgreen" = sRGB24read "#98971a"
+gruvColors "green" = sRGB24read "#b8bb26"
+gruvColors "darkyellow" = sRGB24read "#d79921"
+gruvColors "yellow" = sRGB24read "#fabd2f"
+gruvColors "darkblue" = sRGB24read "#458588"
+gruvColors "blue" = sRGB24read "#83a598"
+gruvColors "brightblue" = sRGB24read "#2e9ef4"
+gruvColors "darkmagenta" = sRGB24read "#b16286"
+gruvColors "magenta" = sRGB24read "#d3869b"
+gruvColors "darkcyan" = sRGB24read "#689d6a"
+gruvColors "cyan" = sRGB24read "#8ec07c"
+gruvColors "lightgrey" = sRGB24read "#a89984"
+gruvColors "white" = sRGB24read "#ebdbb2"
diff --git a/src/Print.hs b/src/Print.hs
new file mode 100644
--- /dev/null
+++ b/src/Print.hs
@@ -0,0 +1,72 @@
+{- Print
+Gregory W. Schwartz
+
+Collections the functions pertaining to printing the ITD output.
+-}
+
+{-# LANGUAGE BangPatterns #-}
+{-# LANGUAGE OverloadedStrings #-}
+
+module Print
+ ( printITD
+ ) where
+
+-- Standard
+import Data.Maybe
+
+-- Cabal
+import qualified Data.ByteString.Char8 as C
+import qualified Data.ByteString.Lazy.Char8 as CL
+import qualified Text.Show.ByteString as CS
+import Data.Fasta.ByteString
+
+-- Local
+import Types
+
+-- | Put the ITD type in a record to be converted to a csv row
+printITD :: Label
+ -> Position
+ -> FastaSequence
+ -> Classification
+ -> ITD
+ -> PrintITD
+printITD (Label l) p fs classification itd =
+ PrintITD { label = l
+ , fHeader = fastaHeader fs
+ , fSequence = fastaSeq fs
+ , dSubstring = fromMaybe ""
+ . fmap (unSubstring . _dupSubstring)
+ . _duplication
+ $ itd
+ , dLocations = fromMaybe ""
+ . fmap (possToString p . _dupLocations)
+ . _duplication
+ $ itd
+ , dMutations = fromMaybe ""
+ . fmap (possToString p . _dupMutations)
+ . _duplication
+ $ itd
+ , sSubstring = fromMaybe ""
+ . fmap (unSubstring . _spacerSubstring)
+ . _spacer
+ $ itd
+ , sLocation =
+ fromMaybe ""
+ . fmap (posToString p . _spacerLocation)
+ . _spacer
+ $ itd
+ , sOtherLocations = fromMaybe ""
+ . fmap (possToString p . _spacerOtherLocations)
+ . _spacer
+ $ itd
+ , classification = C.pack . show $ classification
+ }
+
+-- | Convert a list of positions to a string.
+possToString :: Position -> [Position] -> C.ByteString
+possToString p = C.intercalate "/" . fmap (posToString p)
+
+-- | Convert a position to a string. Add the starting point of the read
+-- (converts to 1 indexed).
+posToString :: Position -> Position -> C.ByteString
+posToString p = CL.toStrict . CS.show . unPosition . (+ p)
diff --git a/src/Repeated.hs b/src/Repeated.hs
new file mode 100644
--- /dev/null
+++ b/src/Repeated.hs
@@ -0,0 +1,208 @@
+{- Repeated
+Gregory W. Schwartz
+
+Collections the functions pertaining to finding the longest repeated substring
+-}
+
+{-# LANGUAGE BangPatterns #-}
+
+module Repeated
+ ( longestRepeatedSubstring
+ , longestRepeatedSubstringMutations
+ ) where
+
+-- Standard
+import Control.Monad
+import Data.List
+import Data.Maybe
+import Data.Ord
+import qualified Data.Map as Map
+import qualified Data.Set as Set
+
+-- Cabal
+import Control.Lens
+import Data.ByteString.Search
+import Data.Fasta.ByteString
+import Safe
+import qualified Data.ByteString.Char8 as C
+import qualified Data.SuffixTree as ST
+
+-- Local
+import Types
+import Utility
+
+longestRepeatedSubstringMutations :: RepeatConfig
+ -> [Position]
+ -> Query
+ -> Maybe LongestSubstring
+longestRepeatedSubstringMutations config muts q = do
+ longest <-
+ longestRepeatedSubstring config q
+
+ result <-
+ case ( _minMut config
+ , getNextLongestF longest, getNextLongestB longest
+ ) of
+ (Nothing, _, _) -> Just longest
+ (_, Nothing, Nothing) -> addMuts longest
+ (Just (MinMut mm), forward, backward) ->
+ if substringLen (forBackBetter forward backward)
+ - substringLen longest < mm
+ then addMuts longest
+ else longestRepeatedSubstringMutations
+ config
+ (snd . (forBackQuery forward backward) longest $ q)
+ . fst
+ $ (forBackQuery forward backward) longest q
+
+ return result
+ where
+ forBackQuery (Just x) Nothing = newQuery mutateQueryForward
+ forBackQuery Nothing (Just x) = newQuery mutateQueryBackward
+ forBackQuery (Just forward) (Just backward) =
+ if substringLen forward >= substringLen backward
+ then newQuery mutateQueryForward
+ else newQuery mutateQueryBackward
+ forBackBetter Nothing (Just backward) = backward
+ forBackBetter (Just forward) Nothing = forward
+ forBackBetter (Just forward) (Just backward) =
+ if substringLen forward >= substringLen backward
+ then forward
+ else backward
+ addMuts = Just
+ . LongestSubstring
+ . over dupMutations (++ muts)
+ . unLongestSubstring
+ substringLen =
+ C.length . unSubstring . _dupSubstring . unLongestSubstring
+ getNextLongestF l =
+ longestRepeatedSubstring config
+ . fst
+ . newQuery mutateQueryForward l
+ $ q
+ getNextLongestB l =
+ longestRepeatedSubstring config
+ . fst
+ . newQuery mutateQueryBackward l
+ $ q
+ newQuery f (LongestSubstring l) = f
+ (head . _dupLocations $ l)
+ (last . _dupLocations $ l)
+ (_dupSubstring l)
+
+-- | Mutate the query by replacing a location in the query with the new
+-- substring
+mutateQueryForward :: Position
+ -> Position
+ -> Substring
+ -> Query
+ -> (Query, [Position])
+mutateQueryForward (Position i) (Position j) (Substring s) (Query q) =
+ if (i + C.length s >= j) || (j + C.length s >= C.length q)
+ then (Query q, [])
+ else ( Query . C.concat $ [beginning, new, middle, new, end]
+ , [Position $ i + C.length s, Position $ j + C.length s]
+ )
+ where
+ beginning = C.take i q
+ middle = C.take (j - (i + C.length s + 1))
+ . C.drop (i + C.length s + 1)
+ $ q
+ end = C.drop (j + C.length s + 1) $ q
+ new = C.append s (C.take 1 . C.drop (j + C.length s) $ q)
+
+-- | Mutate the query by replacing a location in the query with the new
+-- substring
+mutateQueryBackward :: Position
+ -> Position
+ -> Substring
+ -> Query
+ -> (Query, [Position])
+mutateQueryBackward (Position i) (Position j) (Substring s) (Query q) =
+ if i == 0 || j <= i + C.length s - 1
+ then (Query q, [])
+ else ( Query . C.concat $ [beginning, new, middle, new, end]
+ , [Position $ i - 1, Position $ j - 1]
+ )
+ where
+ beginning = C.take (i - 1) q
+ middle = C.take (j - (i + C.length s) - 1) . C.drop (i + C.length s) $ q
+ end = C.drop (j + C.length s) $ q
+ new = C.append (C.take 1 . C.drop (i - 1) $ q) s
+
+-- | Return the longest repeated substring of a list, specifically with an
+-- alphabet
+longestRepeatedSubstring :: RepeatConfig -> Query -> Maybe LongestSubstring
+longestRepeatedSubstring config (Query q) =
+ longestNonOverlap (Query q)
+ . filter checkThresholds
+ . sortBy (comparing snd)
+ . substringRankings
+ . ST.constructWith (_alphabet config)
+ . C.unpack
+ . (flip C.snoc '$')
+ $ q
+ where
+ checkThresholds x =
+ ((>= (unMinSize $ _minSize config)) . C.length . unSubstring . fst $ x)
+ && (checkRichness x)
+ && (checkFalsePositive x)
+ && (maybe True (checkReference x) . _refMap $ config)
+ checkFalsePositive = not
+ . itdFalsePositive (_blacklist config) (_distance config)
+ . C.unpack
+ . unSubstring
+ . fst
+ checkRichness = (>= (unRichness $ _richness config))
+ . getRichness
+ . C.unpack
+ . unSubstring
+ . fst
+ checkReference x =
+ ((not $ _refCheckFlag config) ||)
+ . not
+ . any ( (> 1)
+ . length
+ . nonOverlappingIndices (unSubstring . fst $ x)
+ . fastaSeq
+ )
+ . unReferenceMap
+
+-- | Get the longest non overlapping substring
+longestNonOverlap :: Query -> [(Substring, Int)] -> Maybe LongestSubstring
+longestNonOverlap q =
+ fmap (LongestSubstring . fst)
+ . maximumByMay (comparing snd)
+ . filter (not . isOverlapping . fst)
+ . fmap (\(!s, !n) -> (makeDuplication q s, n))
+
+-- | Get the non overlapping indices of a substring
+makeDuplication :: Query -> Substring -> Duplication
+makeDuplication (Query q) (Substring s) =
+ Duplication
+ (Substring s)
+ headLastDup
+ []
+ where
+ headLastDup = case [headMay dups, lastMay dups] of
+ [Just x, Just y] -> if x == y then [] else [x, y]
+ _ -> []
+ dups = fmap Position
+ . Set.toList
+ . Set.fromList
+ . flip nonOverlappingIndices q
+ $ s
+
+-- | Check if a substring is overlapping
+isOverlapping :: Duplication -> Bool
+isOverlapping x = null . drop 1 . nub . _dupLocations $ x
+
+-- | Get the deepest substring in a suffix tree
+substringRankings :: ST.STree Char -> [(Substring, Int)]
+substringRankings = map (over _1 (Substring . C.pack)) . go ([], 0)
+ where
+ go acc ST.Leaf = [acc]
+ go acc@(!x, !n) (ST.Node es) = concatMap (check acc) es
+ check acc (_, ST.Leaf) = [acc]
+ check (!x, !n) (!p, !tree) =
+ go (x ++ ST.prefix p, n + (length . ST.prefix) p) tree
diff --git a/src/Spacer.hs b/src/Spacer.hs
new file mode 100644
--- /dev/null
+++ b/src/Spacer.hs
@@ -0,0 +1,233 @@
+{- Spacer
+Gregory W. Schwartz
+
+Collections the functions pertaining to finding the spacer in-between
+duplications.
+-}
+
+{-# LANGUAGE BangPatterns #-}
+{-# LANGUAGE TupleSections #-}
+
+module Spacer
+ ( getSpacer
+ ) where
+
+-- Standard
+import Data.List
+import Data.Maybe
+import Data.Ord
+import qualified Data.Set as Set
+
+-- Cabal
+import Control.Lens
+import Data.ByteString.Search
+import Data.List.CommonSubstring
+import Safe
+import qualified Data.ByteString.Char8 as C
+
+-- Local
+import Types
+import Utility
+import Diffusion
+
+getSpacer :: Window
+ -> Time
+ -> Threshold
+ -> ReferenceSeq
+ -> Duplication
+ -> Query
+ -> Maybe Spacer
+getSpacer window
+ time
+ threshold
+ (ReferenceSeq refSeq)
+ (Duplication { _dupSubstring = s, _dupLocations = [p1, p2] })
+ q
+ | C.null . unSubstring $ spacer = Nothing
+ | otherwise =
+ Just $
+ Spacer { _spacerSubstring = spacer
+ , _spacerLocation = spacerPos
+ , _spacerOtherLocations = otherSpacerPositionsDiffusion
+ window
+ time
+ threshold
+ spacerPos
+ p1
+ p2
+ refSeq
+ s
+ spacer
+ }
+ where
+ spacerPos = Position $ unPosition p1 + dupLen
+ spacer = inbetweenSubstring (Length dupLen) p1 p2 q
+ dupLen = C.length . unSubstring $ s
+
+-- | Change a string to be identical with the one duplication position
+mutateQuery :: Maybe Position -> Substring -> String -> String
+mutateQuery Nothing _ _ = []
+mutateQuery (Just (Position p)) (Substring s) q =
+ concat [beginning, C.unpack s, end]
+ where
+ beginning = take p q
+ end = drop (p + C.length s) $ q
+
+-- | Get the most similar sequence to a base sequence from the left or
+-- right substring, along with the base fragment
+minHammingLeftRight
+ :: C.ByteString
+ -> Substring
+ -> Substring
+ -> Either (Substring, C.ByteString) (Substring, C.ByteString)
+minHammingLeftRight base (Substring s) (Substring spacer) =
+ either (Left . (Substring leftSeq,)) (Right . (Substring rightSeq,))
+ . minimumBy (comparing $ either (hamming leftSeq) (hamming rightSeq))
+ . concat
+ $ [ fmap (Left . unSubstring) . baseFragments $ leftSeq
+ , fmap (Right . unSubstring) . baseFragments $ rightSeq
+ ]
+ where
+ baseFragments xs = fragmentSequenceFiller (Window . C.length $ xs) $ base
+ leftSeq = getLeftRightFull LeftP spacer s
+ rightSeq = getLeftRightFull RightP spacer s
+
+-- | Get the positions that are different between the spacer and the
+-- reference sequence
+otherSpacerPositionsDiffusion :: Window
+ -> Time
+ -> Threshold
+ -> Position
+ -> Position
+ -> Position
+ -> C.ByteString
+ -> Substring
+ -> Substring
+ -> [Position]
+otherSpacerPositionsDiffusion window
+ time
+ (Threshold gaussThresh)
+ (Position spacerPos)
+ (Position p1)
+ (Position p2)
+ base
+ (Substring s)
+ (Substring spacer) =
+ fmap Position
+ . Set.toList
+ . Set.intersection (Set.fromList spacerPoss)
+ . Set.fromList
+ . either (fmap (+ p1)) (fmap (+ spacerPos))
+ . over both atypicalPositions
+ $ minHamming
+ where
+ atypicalPositions =
+ fmap fst
+ . filter snd
+ . zip [0..]
+ . fmap (>= gaussThresh)
+ . unSignal
+ . diffusedSeq
+ diffusedSeq (joinedSubstring, baseFragment) =
+ diffuse window time
+ . mutationSignal baseFragment
+ $ joinedSubstring
+ minHamming = minHammingLeftRight base (Substring s) (Substring spacer)
+ spacerPoss = [spacerPos .. p2 - 1]
+
+-- | Get the positions that are different between the spacer and the
+-- reference sequence
+otherSpacerPositions :: MinSize
+ -> Consecutive
+ -> Position
+ -> Position
+ -> Position
+ -> C.ByteString
+ -> Substring
+ -> Substring
+ -> [Position]
+otherSpacerPositions (MinSize minAtypicalSize)
+ consecutive
+ (Position spacerPos)
+ (Position p1)
+ (Position p2)
+ base
+ (Substring s)
+ (Substring spacer)
+ | consecutiveSpacerFalsePositive consecutive base
+ . Substring
+ . getLeftRightPortion LeftP spacer
+ $ s
+ = []
+ | consecutiveSpacerFalsePositive consecutive base
+ . Substring
+ . getLeftRightPortion RightP spacer
+ $ s
+ = []
+ | otherwise =
+ fmap Position
+ . Set.toList
+ . Set.difference (Set.fromList spacerPoss)
+ . Set.intersection (Set.fromList spacerPoss)
+ . Set.fromList
+ . commonPos
+ $ commonStart
+ where
+ commonPos Nothing = []
+ commonPos (Just (Left (Length l))) = [p1 + C.length s - 1 .. p2 - l - 1]
+ commonPos (Just (Right (Length l))) = [spacerPos + l .. p2 - 1]
+ commonStart = headMay
+ . catMaybes
+ . fmap ( leftOrRightFound
+ (Substring base)
+ (Substring spacer)
+ (Substring s)
+ . Length
+ )
+ $ [0 .. minLen]
+ minLen = if C.length spacer <= minAtypicalSize
+ then (-1)
+ else C.length spacer - minAtypicalSize
+ spacerPoss = [spacerPos .. p2 - 1]
+
+-- | Whether the left or right substring is found in the sequence
+leftOrRightFound :: Substring
+ -> Substring
+ -> Substring
+ -> Length
+ -> Maybe (Either Length Length)
+leftOrRightFound (Substring base) (Substring spacer) (Substring s) (Length l) =
+ if C.isInfixOf newString1 base
+ then Just . Left . Length $ l
+ else if C.isInfixOf newString2 base
+ then Just . Right . Length $ l
+ else Nothing
+ where
+ newString1 = C.reverse . C.drop l . C.reverse $ original1
+ newString2 = C.drop l original2
+ original1 = getLeftRightPortion LeftP spacer s
+ original2 = getLeftRightPortion RightP spacer s
+
+-- | Get the string plus a the entirety of another string and
+-- concatenate them
+getLeftRightFull :: LeftRightPortion
+ -> C.ByteString
+ -> C.ByteString
+ -> C.ByteString
+getLeftRightFull LeftP x y = C.append y x
+getLeftRightFull RightP x y = C.append x y
+
+-- | Get the string plus a portion (1 / 3) of another string and
+-- concatenate them
+getLeftRightPortion :: LeftRightPortion
+ -> C.ByteString
+ -> C.ByteString
+ -> C.ByteString
+getLeftRightPortion LeftP x y =
+ C.append (C.drop (2 * (C.length y `div` 3)) y) x
+getLeftRightPortion RightP x y = C.append x . C.take (C.length y `div` 3) $ y
+
+-- | Find the string inbetween two indices of the duplication
+inbetweenSubstring :: Length -> Position -> Position -> Query -> Substring
+inbetweenSubstring (Length n) (Position x) (Position y) =
+ Substring . C.take (y - x - n) . C.drop (x + n) . unQuery
diff --git a/src/Types.hs b/src/Types.hs
new file mode 100644
--- /dev/null
+++ b/src/Types.hs
@@ -0,0 +1,119 @@
+{- Types
+Gregory W. Schwartz
+
+Collections the types used in the program
+-}
+
+{-# LANGUAGE TemplateHaskell #-}
+{-# LANGUAGE GeneralizedNewtypeDeriving #-}
+{-# LANGUAGE DeriveGeneric #-}
+
+module Types where
+
+-- Standard
+import GHC.Generics
+import qualified Data.Map.Strict as Map
+import qualified Data.Set as Set
+
+-- Cabal
+import Control.Lens
+import Data.Csv
+import Data.Fasta.ByteString
+import qualified Data.ByteString.Char8 as C
+import qualified Data.SuffixTree as ST
+import Data.Colour.SRGB
+
+-- Local
+
+-- Algebraic
+newtype Position = Position { unPosition :: Int }
+ deriving (Eq, Show, Num)
+newtype LongestSubstring = LongestSubstring
+ { unLongestSubstring :: Duplication }
+ deriving (Show)
+newtype Query = Query { unQuery :: C.ByteString } deriving (Show)
+newtype Substring = Substring { unSubstring :: C.ByteString }
+ deriving (Eq, Show)
+newtype Length = Length Int deriving (Show)
+newtype Distance = Distance Int deriving (Show)
+newtype Threshold = Threshold Double deriving (Show)
+newtype Percent = Percent Double deriving (Show)
+newtype Consecutive = Consecutive Int deriving (Show)
+newtype Label = Label C.ByteString
+newtype MinSize = MinSize { unMinSize :: Int } deriving (Show)
+newtype Richness = Richness { unRichness :: Int } deriving (Show)
+newtype MinMut = MinMut { unMinMut :: Int } deriving (Show)
+newtype MaxMut = MaxMut { unMaxMut :: Int } deriving (Eq, Ord)
+newtype Window = Window Int
+newtype Signal = Signal { unSignal :: [Double] } deriving (Eq, Ord, Show)
+newtype Time = Time Double deriving (Show)
+newtype Field = Field Int deriving (Show)
+newtype Accession = Accession C.ByteString deriving (Show, Eq, Ord)
+newtype Blacklist = Blacklist
+ { unBlacklist :: (Set.Set String)
+ } deriving (Show)
+newtype ReferenceSeq = ReferenceSeq C.ByteString deriving (Show)
+newtype ReferenceMap = ReferenceMap
+ { unReferenceMap :: (Map.Map Accession FastaSequence)
+ } deriving (Show)
+
+data Classification = Typical | Atypical | Normal deriving (Eq, Ord, Read, Show)
+
+data LeftRightPortion = LeftP | RightP deriving (Show)
+
+data Colors = Colors
+ { _colorDupL :: Colour Double
+ , _colorDupR :: Colour Double
+ , _colorMut :: Colour Double
+ , _colorSpacer :: Colour Double
+ , _colorBackground :: Colour Double
+ , _colorForeground :: Colour Double
+ } deriving (Generic)
+
+data Duplication = Duplication { _dupSubstring :: Substring
+ , _dupLocations :: [Position]
+ , _dupMutations :: [Position]
+ }
+ deriving (Show)
+makeLenses ''Duplication
+
+data Spacer = Spacer { _spacerSubstring :: Substring
+ , _spacerLocation :: Position
+ , _spacerOtherLocations :: [Position]
+ }
+ deriving (Show)
+makeLenses ''Spacer
+
+data ITD = ITD { _duplication :: Maybe Duplication
+ , _spacer :: Maybe Spacer
+ }
+ deriving (Show)
+makeLenses ''ITD
+
+data RepeatConfig = RepeatConfig
+ { _blacklist :: !Blacklist
+ , _refMap :: !(Maybe ReferenceMap)
+ , _richness :: !Richness
+ , _distance :: !Distance
+ , _alphabet :: !(ST.Alphabet Char)
+ , _minSize :: !MinSize
+ , _minMut :: !(Maybe MinMut)
+ , _refCheckFlag :: !Bool
+ } deriving (Show)
+makeLenses ''RepeatConfig
+
+data PrintITD = PrintITD { label :: C.ByteString
+ , fHeader :: C.ByteString
+ , fSequence :: C.ByteString
+ , dSubstring :: C.ByteString
+ , dLocations :: C.ByteString
+ , dMutations :: C.ByteString
+ , sSubstring :: C.ByteString
+ , sLocation :: C.ByteString
+ , sOtherLocations :: C.ByteString
+ , classification :: C.ByteString
+ }
+ deriving (Show, Generic)
+
+instance FromNamedRecord PrintITD
+instance ToNamedRecord PrintITD
diff --git a/src/Utility.hs b/src/Utility.hs
new file mode 100644
--- /dev/null
+++ b/src/Utility.hs
@@ -0,0 +1,141 @@
+{- Utility
+Gregory W. Schwartz
+
+Collections the functions of general use in the program.
+-}
+
+{-# LANGUAGE BangPatterns #-}
+{-# LANGUAGE OverloadedStrings #-}
+
+module Utility
+ ( zipMaybe
+ , fragmentSequence
+ , fragmentSequenceFiller
+ , hammingList
+ , hamming
+ , isOverlappingBySubstring
+ , itdFalsePositive
+ , spacerFalsePositive
+ , consecutiveSpacerFalsePositive
+ , isConsecutive
+ , getRichness
+ , ignore
+ ) where
+
+-- Standard
+import Data.Char
+import Data.List
+import Data.Maybe
+import Data.Monoid
+import qualified Data.Foldable as F
+import qualified Data.Set as Set
+
+-- Cabal
+import qualified Data.ByteString.Char8 as C
+import Data.Fasta.ByteString
+import Text.EditDistance
+
+-- Local
+import Types
+
+
+-- | Get the bs that correspond to the Justs in the first list.
+zipMaybe :: [Maybe a] -> [b] -> [Maybe b]
+zipMaybe xs = zipWith test xs
+ where
+ test (Just _) x = Just x
+ test Nothing x = Nothing
+
+-- | Fragment the sequence by a certain window length
+fragmentSequence :: Window -> C.ByteString -> [Substring]
+fragmentSequence (Window w) = go []
+ where
+ go !acc xs
+ | C.null xs = acc
+ | C.length xs < w = acc
+ | otherwise = go (Substring (C.take w xs) : acc)
+ . C.drop 1
+ $ xs
+
+-- | Fragment the sequence by a certain window length, adding filler
+fragmentSequenceFiller :: Window -> C.ByteString -> [Substring]
+fragmentSequenceFiller (Window w) =
+ go [] . flip C.append filler . C.append filler
+ where
+ filler = C.replicate (w - 1) '-'
+ go !acc xs
+ | C.null xs = acc
+ | C.length xs < w = acc
+ | otherwise = go (Substring (C.take w xs) : acc)
+ . C.drop 1
+ $ xs
+
+-- | Get the hamming list between two strings
+hammingList :: C.ByteString -> C.ByteString -> [Bool]
+hammingList xs = C.zipWith (==) xs
+
+-- | Get the hamming distance between two strings
+hamming :: C.ByteString -> C.ByteString -> Int
+hamming xs = length . filter (not . id) . hammingList xs
+
+-- | Check if positions overlap
+isOverlappingByPosition :: Window -> Position -> Position -> Bool
+isOverlappingByPosition (Window w) (Position x) (Position y) = abs (x - y) < w
+
+-- | Check if positions overlap at the substring level
+isOverlappingBySubstring :: Duplication -> Bool
+isOverlappingBySubstring (Duplication s [p1, p2] _) =
+ isOverlappingByPosition (Window $ C.length . unSubstring $ s) p1 p2
+isOverlappingBySubstring _ =
+ error "Multiple locations found when checking for overlap"
+
+-- | Check if a string is a false positive
+itdFalsePositive :: Blacklist -> Distance -> String -> Bool
+itdFalsePositive (Blacklist blacklist) (Distance d) dup =
+ F.any ((<= d) . levenshteinDistance defaultEditCosts dup) blacklist
+
+-- | Check if the spacer is a false positive based on the Levenshtein
+-- distance (ignoring the insertions and deletions). The threshold here is
+-- a percentage of the spacer with a portion of the duplication (how much
+-- of that string differs).
+spacerFalsePositive :: Percent -> C.ByteString -> Substring -> Bool
+spacerFalsePositive (Percent p) base (Substring s) =
+ (<= (p / 100))
+ . ( \x -> (fromIntegral x - expectedDistance)
+ / (fromIntegral $ C.length s)
+ )
+ . levenshteinDistance defaultEditCosts (C.unpack base)
+ . C.unpack
+ $ s
+ where
+ expectedDistance = fromIntegral $ C.length base - C.length s
+
+-- | Check if the spacer is a false positive based on the Levenshtein
+-- distance (ignoring the insertions and deletions). The threshold here is
+-- a percentage of the spacer with a portion of the duplication (how much
+-- of that string differs).
+consecutiveSpacerFalsePositive :: Consecutive
+ -> C.ByteString
+ -> Substring
+ -> Bool
+consecutiveSpacerFalsePositive (Consecutive c) base (Substring s) =
+ any (not . isConsecutive c . hammingList s . unSubstring)
+ . fragmentSequence (Window . C.length $ s)
+ $ base
+
+-- | See if any x elements are false and neighboring in a list
+isConsecutive :: Int -> [Bool] -> Bool
+isConsecutive c = any (\x -> ((>= c) $ length x) && (not $ head x)) . group
+
+-- | Get the richness of a list.
+getRichness :: (Eq a, Ord a) => [a] -> Int
+getRichness = Set.size . Set.fromList
+
+-- | Check to see if a fasta sequence should be analyzed.
+ignore :: Int -> FastaSequence -> Maybe FastaSequence
+ignore field fs = case getField field '|' fs of
+ "0" -> Nothing
+ "1" -> Just fs
+ _ -> error
+ $ "ignore-field process: neither a 0 nor 1 found at position "
+ <> show field