diff --git a/LICENSE b/LICENSE new file mode 100644 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. 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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 +1,686 @@ +{- heatitup-complete +Gregory W. Schwartz + +Find duplications a sequence with assembly. Requires all to be in path: +heatitup, Trinity, samtools (if input is a bam), rsem-prepare-reference, +rsem-calculate-expression, and bowtie2. Cleans up at the end by deleting all +files with INPUT.* pattern, the new period being the main difference. +-} + +{-# LANGUAGE ViewPatterns #-} +{-# LANGUAGE OverloadedStrings #-} + +module Main where + +-- Standard +import Data.Bool +import Data.Maybe +import qualified Data.List.NonEmpty as NE +import qualified Data.Map.Strict as Map +import qualified Data.Set as Set + +-- Cabal +import Data.Fasta.Text +import Pipes +import qualified Pipes.Prelude as P +import qualified Pipes.Text as PT +import qualified Pipes.Text.IO as PT +import qualified Control.Foldl as Fold +import qualified Data.ByteString.Lazy.Char8 as B +import qualified Data.Csv as CSV +import qualified Data.Text as T +import qualified Data.Vector as V +import qualified Options.Applicative as O +import Turtle +import Turtle.Line + +-- Local +import Types +import Parse +import Merge +import Blast +import Utility + +-- | Command line arguments +data Options = Options { input :: String + , spacerFlag :: Bool + , refInput :: Maybe String + , blacklistInput :: Maybe String + , output :: Maybe String + , outputPlot :: Maybe String + , 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 + , preprocessType :: Preprocess + , blastCommand :: Maybe String + , blastArgs :: Maybe String + , trinityCommand :: String + , trinityArgs :: TrinityArgs + , trinityAbundance :: String + , dirtyFlag :: Bool + , cigarFlag :: Bool + , headers :: Maybe String + } + +-- | Command line options +options :: O.Parser Options +options = Options + <$> O.strOption + ( O.long "input" + <> O.short 'i' + <> O.metavar "FILE" + <> O.help "The input file" + ) + <*> O.switch + ( O.long "spacer" + <> O.short 's' + <> O.help "Whether to characterize the spacer. Requires\ + \ reference-input and matching labels for the input and\ + \ reference-input to compare." + ) + <*> O.optional ( O.strOption + ( O.long "reference-input" + <> O.short 'I' + <> O.metavar "[Nothing] | FILE" + <> O.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." + ) + ) + <*> O.optional ( O.strOption + ( O.long "blacklist-input" + <> O.short 'b' + <> O.metavar "[Nothing] | FILE" + <> O.help "The input fasta file containing possible false positives --\ + \ sequences which may be duplicate nucleotides in the\ + \ reference sequence." + ) + ) + <*> O.optional ( O.strOption + ( O.long "output" + <> O.short 'o' + <> O.metavar "FILE" + <> O.help "The output file" + ) + ) + <*> O.optional ( O.strOption + ( O.long "output-plot" + <> O.short 'O' + <> O.metavar "FILE" + <> O.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." + ) + ) + <*> O.strOption + ( O.long "label" + <> O.short 'l' + <> O.metavar "STRING" + <> O.value "" + <> O.help "The label to use in the label column for the output" + ) + <*> O.option O.auto + ( O.long "reference-field" + <> O.short 'f' + <> O.metavar "[1] | INT" + <> O.value 1 + <> O.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." + ) + <*> O.optional ( O.option O.auto + ( O.long "position-field" + <> O.short 'p' + <> O.metavar "[Nothing] | INT" + <> O.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." + ) + ) + <*> O.optional ( O.option O.auto + ( O.long "ignore-field" + <> O.short 'g' + <> O.metavar "[Nothing] | INT" + <> O.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." + ) + ) + <*> O.option O.auto + ( O.long "min-size" + <> O.short 's' + <> O.metavar "[15] | INT" + <> O.value 15 + <> O.help "The minimum size of a duplication" + ) + <*> O.option O.auto + ( O.long "gaussian-window" + <> O.short 'w' + <> O.metavar "[4] | Double" + <> O.value 3 + <> O.help "The window for the discrete gaussian kernel atypical spacer\ + \ determination" + ) + <*> O.option O.auto + ( O.long "gaussian-time" + <> O.short 't' + <> O.metavar "[2] | Double" + <> O.value 2 + <> O.help "The time for the discrete gaussian kernel atypical spacer\ + \ determination" + ) + <*> O.option O.auto + ( O.long "gaussian-threshold" + <> O.short 'T' + <> O.metavar "[0.4] | Double" + <> O.value 0.4 + <> O.help "The cutoff to be considered a mutation for the discrete\ + \ gaussian kernel atypical spacer determination" + ) + <*> O.optional ( O.option O.auto + ( O.long "min-mutations" + <> O.short 'm' + <> O.metavar "INT" + <> O.help "The minimum number of nucleotides between mutations" + ) + ) + <*> O.option O.auto + ( O.long "levenshtein-distance" + <> O.short 'L' + <> O.metavar "[2] | INT" + <> O.value 2 + <> O.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" + ) + <*> O.switch + ( O.long "reference-check-blacklist" + <> O.short 'c' + <> O.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." + ) + <*> O.switch + ( O.long "reference-recursive-blacklist" + <> O.short 'r' + <> O.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." + ) + <*> O.option O.auto + ( O.long "min-richness" + <> O.short 'R' + <> O.metavar "[1] | INT" + <> O.value 1 + <> O.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." + ) + <*> O.strOption + ( O.long "color-left-duplication" + <> O.metavar "[#a6cae3] | COLOR" + <> O.help "The color of the left side of the repeated sequence." + <> O.value "#a6cae3" + ) + <*> O.strOption + ( O.long "color-right-duplication" + <> O.metavar "[#b0de8a] | COLOR" + <> O.help "The color of the right side of the repeated sequence." + <> O.value "#b0de8a" + ) + <*> O.strOption + ( O.long "color-difference" + <> O.metavar "[#1978b3] | COLOR" + <> O.help "The color of discrepancies between the left and right side of\ + \ the duplication." + <> O.value "#1978b3" + ) + <*> O.strOption + ( O.long "color-spacer" + <> O.metavar "[#fdbd6e] | COLOR" + <> O.help "The color of the exogenous nucleotides within the spacer." + <> O.value "#fdbd6e" + ) + <*> O.strOption + ( O.long "color-background" + <> O.metavar "[#ffffff] | COLOR" + <> O.help "The color of the background." + <> O.value "#ffffff" + ) + <*> O.strOption + ( O.long "color-foreground" + <> O.metavar "[#000000] | COLOR" + <> O.help "The color of the foreground." + <> O.value "#000000" + ) + <*> O.option O.auto + ( O.long "type" + <> O.short 'P' + <> O.metavar "Assembly | NonAssembly CHAR" + <> O.help "The type of preprocessing before duplication finding.\ + \ Assembly would be used on exome sequencing, RNA-seq, etc.\ + \ while NonAssembly would be for certain paired end\ + \ sequencing like amplicon based. Basically, are the reads\ + \ fragmented across a location (Assembly) or are they\ + \ all piled up (NonAssembly)? Paired end is required for\ + \ NonAssembly, otherwise just use the duplication finding\ + \ program directly on the reads for best results.\ + \ NonAssembly additionally requires a character to use as\ + \ filler between non-overlapping mate pairs, as the\ + \ program will remove duplications containing that\ + \ character. Input would look like \"NonAssembly 'X'\"." + ) + <*> O.optional ( O.strOption + ( O.long "blast-command" + <> O.short 'B' + <> O.metavar "[Nothing] | PATH" + <> O.help "The command used for blastn. Useful if not in path.\ + \ Used for filtering out reads from irrelevant locations.\ + \ If using small sequences, be sure to set blast-args\ + \ to \"-task blastn-short\"." + ) + ) + <*> O.optional ( O.strOption + ( O.long "blast-args" + <> O.short 'z' + <> O.metavar "[Nothing] | STRING" + <> O.help "The additional arguments used for blastn. Separated by space.\ + \ Use \"-task blastn-short\" for small sequences." + ) + ) + <*> O.strOption + ( O.long "trinity-command" + <> O.short 'C' + <> O.metavar "[Trinity] | PATH" + <> O.value "Trinity" + <> O.help "The command used for Trinity. Useful if not in path." + ) + <*> O.option O.auto + ( O.long "trinity-args" + <> O.short 'A' + <> O.metavar "[TrinityBase] | TrinityGenome | TrinityCustom STRING" + <> O.value TrinityBase + <> O.help "The arguments used for Trinity.\ + \ TrinityBase is --seqType fq --run_as_paired --max_memory 10G --no_version_check --single,\ + \ TrinityGenome is --genome_guided_max_intron 10000 --max_memory 10G --no_version_check --genome_guided_bam,\ + \ and TrinityCustom STRING is STRING.\ + \ Make sure the input argument\ + \ is last and points to nothing (like in the default)." + ) + <*> O.strOption + ( O.long "trinity-abundance" + <> O.short 'a' + <> O.metavar "[align_and_estimate_abundance.pl] | PATH" + <> O.value "align_and_estimate_abundance.pl" + <> O.help "The command used for align_and_estimate_abundance.pl\ + \ in Trinity's util folder. Useful if not in path. Make sure\ + \ kallisto is in the path." + ) + <*> O.switch + ( O.long "dirty" + <> O.short 'd' + <> O.help "Leave behind the INPUT.* files at the end (but the trinity\ + \ output is still deleted)." + ) + <*> O.switch + ( O.long "no-cigar-filter" + <> O.short 'G' + <> O.help "Skip the CIGAR based filtering, that is, look at all reads\ + \ and not just reads without all M's in the CIGAR." + ) + <*> O.optional ( O.strOption + ( O.long "header" + <> O.short 'H' + <> O.metavar "[Nothing] | STRING" + <> O.help "The headers used when converting bam to fasta.\ + \ The order in the resulting header is\ + \ \">FILE|ACCESSION|POSITION|IGNORE|HEADER\".\ + \ So take that order\ + \ into account for field options with positions and the\ + \ rest. Also, make sure this string has fields separated by\ + \ a pipe \"|\" character. So if you have HEADER as the\ + \ \"ENSE00000SOMETHING\" reference accession that\ + \ agrees with --input-reference, that would be\ + \ field 5." + ) + ) + +-- | Get the Trinity arguments. +defTrinityArgs :: TrinityArgs -> T.Text +defTrinityArgs TrinityBase = T.pack "--seqType fq\ + \ --run_as_paired\ + \ --max_memory 10G\ + \ --no_version_check\ + \ --single" +defTrinityArgs TrinityGenome = T.pack "--genome_guided_max_intron 10000\ + \ --max_memory 10G\ + \ --no_version_check\ + \ --genome_guided_bam" +defTrinityArgs (TrinityCustom x) = T.pack x + +-- | Run the trinity command. +runTrinity :: Options -> Turtle.FilePath -> Turtle.FilePath -> IO () +runTrinity opts tempFile tempDir = do + let modifiedArgs = (T.words . defTrinityArgs . trinityArgs $ opts) + <> [ format fp tempFile + , "--output" + , format fp tempDir + ] + + stderr . inproc (T.pack $ trinityCommand opts) modifiedArgs $ mempty + + return () + +-- | Run samtools if the input is a bam file. +runSamtools :: Options -> Turtle.FilePath -> IO Turtle.FilePath +runSamtools opts tempFasta = do + let inputFile = T.pack . Main.input $ opts + outputType = case preprocessType opts of + Assembly -> "fastq" + (NonAssembly _) -> "fasta" + + fastFile <- if hasExtension (fromText inputFile) "bam" + then strict $ do + Turtle.output tempFasta + . inproc "samtools" [outputType, inputFile] + $ mempty + return . NE.head . textToLines . format fp $ tempFasta + else + return inputFile + + return . fromText . T.strip $ fastFile + +-- | Run the abundance command. +runAlignContig :: Options -> Turtle.FilePath -> Turtle.FilePath -> Shell Line +runAlignContig opts tempDir trinityFastaFile = do + tempFasta <- mktempfile tempDir "trinity.fasta" + + inputFasta <- liftIO . runSamtools opts $ tempFasta + fastaMap <- + fmap (fastaToMap ' ') -- Trinity outputs ' ' as a separator. + . liftIO + . PT.runSafeT + . runEffect + . P.toListM + $ pipesFasta (PT.readFile . T.unpack . format fp $ trinityFastaFile) + + bamOutput <- strict + . inproc "samtools" ["view", "-F", "4", "-"] -- No headers and unmapped reads + . inproc + (T.pack $ trinityAbundance opts) + [ "--transcripts", format fp trinityFastaFile + , "--seqType", "fa" + , "--single", format fp inputFasta + , "--est_method", "kallisto" + , "--kallisto_add_opts", "--pseudobam" + , "--trinity_mode" + , "--prep_reference" + , "--output_dir", format fp tempDir + ] + $ mempty + + let bamRows' = fmap (BamRow . T.splitOn "\t") . T.lines $ bamOutput + + bamRows <- case blastCommand opts of + (Just cmd) -> filterBlastBamRows + 2 + (Command . T.pack $ cmd) + (fmap Args . blastArgs $ opts) + ( Subject + . fromText + . T.pack + . fromMaybe (error "Need --reference-input for blast.") + . refInput + $ opts + ) + (QueryFile trinityFastaFile) + bamRows' + Nothing -> return bamRows' + + let matchMap = getMatchMap bamRows + + select + . concatMap (NE.toList . textToLines) + . concat + . nub' + . fmap + ( bamToFasta + (Just fastaMap) + (bool (Just matchMap) Nothing . cigarFlag $ opts) + (T.pack $ Main.input opts) + (fmap (Headers . T.pack) . headers $ opts) + ) + $ bamRows + +-- | Find duplications in the Trinity output. +runFindDuplication :: Options -> Shell Line -> Shell Line +runFindDuplication opts streamIn = + inproc "heatitup" commandList streamIn + where + commandList = + fmap T.pack + . concat + . catMaybes + $ [ fmap (("--reference-input" :) . (:[])) . refInput $ opts + , bool Nothing (Just ["--spacer"]) . spacerFlag $ opts + , fmap (("--blacklist-input" :) . (:[])) . blacklistInput $ opts + , fmap (("--output" :) . (:[])) . Main.output $ opts + , fmap (("--output-plot" :) . (:[])) . outputPlot $ opts + , Just ["--label", outputLabel opts] + , Just ["--reference-field", show . refField $ opts] + , fmap (("--position-field" :) . (:[]) . show) . posField $ opts + , fmap (("--ignore-field" :) . (:[]) . show) . ignoreField $ opts + , Just ["--min-size", show . inputMinSize $ opts] + , Just ["--gaussian-window", show . gaussWindow $ opts] + , Just ["--gaussian-time", show . gaussTime $ opts] + , Just ["--gaussian-threshold", show . gaussThreshold $ opts] + , fmap (("--min-mutations" :) . (:[]) . show) . inputMinMut $ opts + , Just ["--levenshtein-distance", show . inputDistance $ opts] + , bool Nothing (Just ["--reference-check-blacklist"]) + . refCheckBlacklistFlag + $ opts + , bool Nothing (Just ["--reference-recursive-blacklist"]) + . refRecBlacklistFlag + $ opts + , Just ["--min-richness", show . minRichness $ opts] + , Just ["--color-left-duplication", inputColorDupL $ opts] + , Just ["--color-right-duplication", inputColorDupR $ opts] + , Just ["--color-difference", inputColorMut $ opts] + , Just ["--color-spacer", inputColorSpacer $ opts] + , Just ["--color-background", inputColorBackground $ opts] + , Just ["--color-foreground", inputColorForeground $ opts] + ] + + +-- | Cleanup the intermediate files. +cleanup :: Options -> Shell () +cleanup opts = sh $ do + removableHere <- + fold ( grep (has . text $ T.pack (Main.input opts) <> ".") + . join + . fmap (select . textToLines . format fp) + . ls + $ "." + ) + Fold.list + removableThere <- + fold ( grep (has . text $ T.pack (Main.input opts) <> ".") + . join + . fmap (select . textToLines . format fp) + . ls + . directory + . fromText + . T.pack + . Main.input + $ opts + ) + Fold.list + + mapM_ (rm . fromText . lineToText) $ removableHere <> removableThere + + return () + +assembly :: Options -> IO () +assembly opts = sh $ do + tempDir <- mktempdir "." "trinity" + tempFile' <- mktempfile "." "tmp.fq" + tempFile <- + case trinityArgs opts of + TrinityBase -> liftIO . runSamtools opts $ tempFile' + TrinityGenome -> + return . fromText . T.pack . Main.input $ opts + (TrinityCustom _) -> + return . fromText . T.pack . Main.input $ opts + + liftIO . runTrinity opts tempFile $ tempDir + trinityFastaFile <- + fold (find (has "/Trinity" <> suffix ".fasta") tempDir) Fold.head + + _ <- if isNothing trinityFastaFile + then error "Fasta not generated." + else return () + + duplicationOutput <- strict + . runFindDuplication opts + . runAlignContig opts tempDir + . fromJust + $ trinityFastaFile + + unless (dirtyFlag opts) . cleanup $ opts + + abundances <- + strict + . maybe mempty (Turtle.input . const (tempDir "abundance.tsv")) + $ trinityFastaFile + + unless (dirtyFlag opts) . cleanup $ opts + + let abundanceMap' = getAbundanceMap . B.pack . T.unpack $ abundances + (dupHeader, dupRows) = + parseDuplications . B.pack . T.unpack $ duplicationOutput + accSet = getAccSet dupRows + abundanceMap = --We only want the frequency of valid contigs + AbundanceMap + . Map.filterWithKey (\k _ -> Set.member k . unAccSet $ accSet) + . unAbundanceMap + $ abundanceMap' + frequencyMap = getFrequencyMap abundanceMap + newRows = fmap (mergeAbundance frequencyMap) dupRows + finalOutput = CSV.encodeByName (V.snoc dupHeader "frequency") + . fmap unDuplicationRow + $ newRows + + liftIO . B.putStrLn $ finalOutput + +-- | Remove rows where the duplication contains the filler. +removeFillDups :: Fill -> WithHeader Line -> Maybe Line +removeFillDups _ (Header x) = Just x +removeFillDups (Fill fill) (Row h row) = + if T.isInfixOf (T.singleton fill) + . fromMaybe (error "dSubstring column not found.") + . lookup "dSubstring" + . zip (getCols h) + . getCols + $ row + then Nothing + else Just row + where + getCols = T.splitOn "," . lineToText + +nonAssembly :: Options -> Fill -> IO () +nonAssembly opts fill = sh $ do + bamOutput <- strict + . inproc "samtools" ["view", "-"] -- No headers + . inproc "samtools" [ "sort" + , "-n" + , "-O", "sam" + , T.pack $ Main.input opts + ] + $ mempty + + let bamRows' = parseBAM bamOutput + query = QueryShell + . select + . concatMap (NE.toList . textToLines) + . concatMap blastBamToFasta + $ bamRows' + + -- Get rid of sequences that don't blast to the reference. + bamRows <- case blastCommand opts of + (Just cmd) -> filterBlastBamRows + 0 + (Command . T.pack $ cmd) + (fmap Args . blastArgs $ opts) + ( Subject + . fromText + . T.pack + . fromMaybe (error "Need --reference-input for blast.") + . refInput + $ opts + ) + query + bamRows' + Nothing -> return bamRows' + + let mergedMates = mergeMates fill bamRows + fastaOutput = select + . concatMap (NE.toList . textToLines) + . concatMap ( bamToFasta + Nothing + Nothing + (T.pack $ Main.input opts) + (fmap (Headers . T.pack) . headers $ opts) + ) + $ mergedMates + + stdout + . fmap fromJust + . mfilter isJust + . fmap (removeFillDups fill) + . Turtle.header + . runFindDuplication opts + $ fastaOutput + +mainFunc :: Options -> IO () +mainFunc opts@(preprocessType -> Assembly) = assembly opts +mainFunc opts@(preprocessType -> NonAssembly fill) = + nonAssembly opts (Fill fill) + +main :: IO () +main = O.execParser opts >>= mainFunc + where + opts = O.info (O.helper <*> Main.options) + ( O.fullDesc + <> O.progDesc "Finds duplications in a sequence with assembly" + <> O.header "heatitup-complete, Gregory W. Schwartz" ) diff --git a/heatitup-complete.cabal b/heatitup-complete.cabal new file mode 100644 --- /dev/null +++ b/heatitup-complete.cabal @@ -0,0 +1,60 @@ +name: heatitup-complete +version: 0.5.3.3 +synopsis: Find and annotate ITDs with assembly or read pair joining. +description: Find and annotate ITDs with assembly or read pair joining using suffix trees and characterize the exogenous segments within the spacer using heat diffusion. +homepage: http://github.com/GregorySchwartz/heatitup-complete#readme +license: GPL-3 +license-file: LICENSE +author: Gregory W. Schwartz +maintainer: gsch@pennmedicine.upenn.edu +copyright: Copyright: (c) 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 + , Parse + , Merge + , Blast + build-depends: base >= 4.7 && < 5 + , bytestring + , cassava + , containers + , fasta + , foldl + , lens + , safe + , text + , text-show + , turtle + , vector + ghc-options: -O2 + default-language: Haskell2010 + +executable heatitup-complete + hs-source-dirs: app + main-is: Main.hs + ghc-options: -threaded -rtsopts -O2 + build-depends: base + , heatitup-complete + , bytestring + , cassava + , containers + , fasta + , foldl + , optparse-applicative + , pipes + , pipes-text + , safe + , text + , turtle + , vector + default-language: Haskell2010 + +source-repository head + type: git + location: https://github.com/GregorySchwartz/heatitup-complete diff --git a/src/Blast.hs b/src/Blast.hs new file mode 100644 --- /dev/null +++ b/src/Blast.hs @@ -0,0 +1,66 @@ +{- Blast +Gregory W. Schwartz + +Collects the functions pertaining to Blasting sequences. +-} + +{-# LANGUAGE OverloadedStrings #-} + +module Blast + ( filterBlastBamRows + , blastBamToFasta + ) where + +-- Standard +import Data.Maybe +import qualified Data.Set as Set + +-- Cabal +import qualified Control.Foldl as Fold +import qualified Data.Text as T +import Safe +import Turtle +import Turtle.Line + +-- Local +import Types + +-- | Get the accessions that successfully align to the reference. +getBlastSet :: Command -> Maybe Args -> Subject -> Query -> Shell BlastSet +getBlastSet (Command cmd) args (Subject sub) query = do + let queryIn (QueryFile x) = input x + queryIn (QueryShell x) = x + argsIn = maybe [] (fmap T.pack . words . unArgs) args + blastOutput = fmap fromJust + . mfilter isJust + . fmap (headMay . cut "\t" . lineToText) + . inproc cmd ( [ "-subject", format fp sub + , "-outfmt", "6" + , "-max_target_seqs", "1" + ] + <> argsIn + ) + . queryIn + $ query + blastSet <- fmap (BlastSet . Set.fromList) . fold blastOutput $ Fold.list + + return blastSet + +-- | Filter out BamRows that do not successfully align to the reference. +filterBlastBamRows :: Int -> Command -> Maybe Args -> Subject -> Query -> [BamRow] -> Shell [BamRow] +filterBlastBamRows accField cmd args sub query rows = do + blastSet <- getBlastSet cmd args sub $ query + + let newRows = + filter + (flip Set.member (unBlastSet blastSet) . (`at` accField) . unBamRow) + rows + + return newRows + +-- | Convert a bam row to fasta for a quick blast check. +blastBamToFasta :: BamRow -> [T.Text] +blastBamToFasta (BamRow row) = + [ ">" <> (fromMaybe (error "No accession in bam.") . headMay $ row) + , fromMaybe (error "No sequence in bam.") $ row `atMay` 9 + ] diff --git a/src/Merge.hs b/src/Merge.hs new file mode 100644 --- /dev/null +++ b/src/Merge.hs @@ -0,0 +1,113 @@ +{- Merge +Gregory W. Schwartz + +Collects the functions pertaining to the merging of headers with abundances. +-} + +{-# LANGUAGE BangPatterns #-} +{-# LANGUAGE OverloadedStrings #-} + +module Merge + ( mergeAbundance + , mergeMates + , bamToFasta + ) where + +-- Standard +import Data.Function (on) +import Data.List +import Data.Maybe +import Data.Monoid +import qualified Data.IntMap.Strict as IMap +import qualified Data.Map.Strict as Map + +-- Cabal +import Control.Lens +import qualified Data.Text as T +import qualified Data.Text.Read as T +import Safe +import TextShow + +-- Local +import Types +import Utility + +mergeAbundance :: FrequencyMap -> DuplicationRow -> DuplicationRow +mergeAbundance (FrequencyMap m) (DuplicationRow row) = + DuplicationRow + . Map.insert "frequency" (showt . findWithError rowAccession $ m) + $ row + where + rowAccession = + flip (Safe.at) 1 . T.splitOn "|" . findWithError "fHeader" $ row + +-- | Get the position map of a sequence. +getPositionMap :: Position -> Sequence -> PositionMap +getPositionMap (Position p) = + PositionMap . IMap.fromList . zip [p..] . T.unpack . unSequence + +-- | Fill the gaps in a position sequence list with a character. +fillGapsWith :: Fill + -> [(Position, Char)] + -> [(Position, Char)] + -> [(Position, Char)] +fillGapsWith _ !acc [] = reverse acc +fillGapsWith fill [] (x:xs) = fillGapsWith fill [x] xs +fillGapsWith + fill + acc@((Position !previousPos, _):_) + allNext@((Position !currentPos, !currentChar):xs) = + if abs (currentPos - previousPos) > 1 + then fillGapsWith + fill + ((Position (previousPos + 1), unFill fill) : acc) + allNext + else fillGapsWith + fill + ((Position currentPos, currentChar) : acc) + xs + +-- | Merge two sequences by their positions. +mergeSequences :: Fill + -> (Position, Sequence) + -> (Position, Sequence) + -> Sequence +mergeSequences fill left = + Sequence + . T.pack + . fmap snd + . fillGapsWith fill [] + . fmap (over _1 Position) + . IMap.toAscList + . IMap.union (unPositionMap . uncurry getPositionMap $ left) + . unPositionMap + . uncurry getPositionMap + +-- | Merge a mate pair. Assumes that the lines are sorted by mate pair already +-- (samtools sort -n). Also assumes that the left mate appears first. Removes +-- supplementary alignments. +mergePair :: Fill -> [BamRow] -> Maybe BamRow +mergePair fill xs = + case filter (not . isSupplementary) xs of + [] -> Nothing + [x] -> Just x + [BamRow left, BamRow right] -> + Just + . BamRow + . set (ix 9) ( unSequence + $ mergeSequences fill (posSeq left) (posSeq right) + ) + $ left + xs -> error ("Too many mate pairs (even after supplementary removal) for: " <> show xs) + where + posSeq xs = ( either error (Position . fst) . T.decimal $ xs !! 3 + , Sequence $ xs !! 9 + ) + isSupplementary = + (== "1") . drop 11 . decodeSAMFlag . read . T.unpack . (!! 1) . unBamRow + +-- | Merge all mate pairs. Assumes that the lines are sorted by mate pair already +-- (samtools sort -n). +mergeMates :: Fill -> [BamRow] -> [BamRow] +mergeMates fill = + catMaybes . fmap (mergePair fill) . groupBy ((==) `on` (head . unBamRow)) diff --git a/src/Parse.hs b/src/Parse.hs new file mode 100644 --- /dev/null +++ b/src/Parse.hs @@ -0,0 +1,75 @@ +{- Parse +Gregory W. Schwartz + +Collects the functions pertaining to the parsing of the abundance output. +-} + +{-# LANGUAGE BangPatterns #-} +{-# LANGUAGE OverloadedStrings #-} + +module Parse + ( getAbundanceMap + , getFrequencyMap + , getAccSet + , parseDuplications + , parseBAM + ) where + +-- Standard +import Data.Char +import qualified Data.Map.Strict as Map +import qualified Data.Set as Set + +-- Cabal +import Control.Lens +import Data.Csv +import Data.Text.Read +import qualified Data.ByteString.Lazy.Char8 as B +import qualified Data.Text as T +import qualified Data.Vector as V +import Safe + +-- Local +import Types +import Utility + +-- | Get the abundance map from the contents of the abundance output. +getAbundanceMap :: B.ByteString -> AbundanceMap +getAbundanceMap = + AbundanceMap + . Map.unions + . fmap (\ !m -> Map.singleton + (findWithError ("target_id" :: T.Text) m) + (getDouble . findWithError ("est_counts" :: T.Text) $ m) + ) + . V.toList + . either error snd + . decodeByNameWith decodeOpts + where + decodeOpts = defaultDecodeOptions { decDelimiter = fromIntegral (ord '\t') } + getDouble = either error fst . double + +-- | Convert an abundance map to a frequency map. +getFrequencyMap :: AbundanceMap -> FrequencyMap +getFrequencyMap (AbundanceMap m) = FrequencyMap . Map.map (/ totalCount) $ m + where + totalCount = Map.foldl (+) 0 m + +-- | Get the list of accessions from a duplication row post-Trinity. +getAccSet :: [DuplicationRow] -> AccSet +getAccSet = AccSet + . Set.fromList + . fmap ( flip (Safe.at) 1 + . T.splitOn "|" + . findWithError "fHeader" + . unDuplicationRow + ) + +-- | Get the duplications in an easy to read format. +parseDuplications :: B.ByteString -> (Header, [DuplicationRow]) +parseDuplications = + over _2 (fmap DuplicationRow . V.toList) . either error id . decodeByName + +-- | Parse bam rows. +parseBAM :: T.Text -> [BamRow] +parseBAM = fmap (BamRow . T.splitOn "\t") . T.lines diff --git a/src/Types.hs b/src/Types.hs new file mode 100644 --- /dev/null +++ b/src/Types.hs @@ -0,0 +1,76 @@ +{- Types +Gregory W. Schwartz + +Collects the types used in the program +-} + +module Types where + +-- Standard +import qualified Data.IntMap.Strict as IMap +import qualified Data.Map.Strict as Map +import qualified Data.Set as Set + +-- Cabal +import qualified Data.Text as T +import Turtle + +-- Local + + +-- Algebraic +data Preprocess = Assembly | NonAssembly Char deriving (Read, Show) +data TrinityArgs = TrinityBase | TrinityGenome | TrinityCustom String deriving (Read, Show) +data Query = QueryFile Turtle.FilePath | QueryShell (Shell Line) + +-- Basic +newtype Position = Position + { unPosition :: Int + } deriving (Show) +newtype Sequence = Sequence + { unSequence :: T.Text + } deriving (Show) +newtype Fill = Fill + { unFill :: Char + } deriving (Show) +newtype Command = Command + { unCommand :: T.Text + } deriving (Show) +newtype Args = Args + { unArgs :: String + } deriving (Show) +newtype Subject = Subject + { unSubject :: Turtle.FilePath + } deriving (Show) + +-- Advanced +newtype BamRow = BamRow + { unBamRow :: [T.Text] + } deriving (Read, Show) +newtype Headers = Headers + { unHeaders :: T.Text + } +newtype AbundanceMap = AbundanceMap + { unAbundanceMap :: Map.Map T.Text Double + } +newtype FrequencyMap = FrequencyMap + { unFrequencyMap :: Map.Map T.Text Double + } +newtype DuplicationRow = DuplicationRow + { unDuplicationRow :: Map.Map T.Text T.Text + } +newtype PositionMap = PositionMap + { unPositionMap :: IMap.IntMap Char + } +newtype AccessionMap = AccessionMap + { unAccessionMap :: Map.Map T.Text T.Text + } deriving (Read, Show) +newtype BlastSet = BlastSet + { unBlastSet :: Set.Set T.Text + } +newtype AccSet = AccSet + { unAccSet :: Set.Set T.Text + } +newtype MatchMap = MatchMap + { unMatchMap :: Map.Map T.Text Bool + } diff --git a/src/Utility.hs b/src/Utility.hs new file mode 100644 --- /dev/null +++ b/src/Utility.hs @@ -0,0 +1,105 @@ +{- Utility +Gregory W. Schwartz + +Collects the functions pertaining to utility helper functions. +-} + +{-# LANGUAGE BangPatterns #-} +{-# LANGUAGE ViewPatterns #-} +{-# LANGUAGE OverloadedStrings #-} + +module Utility + ( findWithError + , bamToFasta + , appendHeader + , fastaToMap + , getMatchMap + , nub' + , decodeSAMFlag + ) where + +-- Standard +import Data.Bool +import Data.Char +import Data.Maybe +import Data.Monoid +import Numeric +import qualified Data.ByteString.Char8 as B +import qualified Data.Map.Strict as Map +import qualified Data.Set as Set + +-- Cabal +import qualified Control.Foldl as Fold +import qualified Data.Text as T +import Data.Fasta.Text +import Safe +import Turtle.Line + +-- Local +import Types + +-- | Return a specific error when the text key is not found. +findWithError :: (Eq a, Ord a, Show a) => a -> Map.Map a b -> b +findWithError x = Map.findWithDefault (error (show x <> " not found.")) x + +-- | Whether to ignore the read based on the cigar (0 is ignore 1 is don't +-- ignore). +isIgnore :: T.Text -> Bool +isIgnore = (== "M") . T.filter isAlpha + +-- | Convert a line in a bam file to a fasta format for duplication input. Uses +-- values from the maps if Assembly. +bamToFasta :: Maybe AccessionMap + -> Maybe MatchMap + -> T.Text + -> Maybe Headers + -> BamRow + -> [T.Text] +bamToFasta aMap mMap fileHeader headers (BamRow row) = + [ ">" <> header + , maybe (row `at` 9) (lookupErr (row `at` 2) . unAccessionMap) aMap + ] + where + header = T.intercalate "|" + . catMaybes + $ [ Just fileHeader + , Just $ if isJust aMap then (row `at` 2) else (row `at` 0) + , Just $ if isJust aMap then "" else (row `at` 3) + , Just . bool "1" "0" + . maybe + (isIgnore $ row `at` 5) + (lookupErr (row `at` 2) . unMatchMap) + $ mMap + , fmap unHeaders headers + ] + +-- | Append a header to the end of the header line in a fasta row. +appendHeader :: Maybe Headers -> Line -> Line +appendHeader Nothing row = row +appendHeader (Just (Headers h)) row@((T.take 1 . lineToText) -> ">") = + unsafeTextToLine $ lineToText row <> "|" <> h +appendHeader _ row = row + +-- | Create a mapping from accession number to sequence. Trinity outputs ' ' as +-- a separator. +fastaToMap :: Char -> [FastaSequence] -> AccessionMap +fastaToMap sep = + AccessionMap . Map.fromList . fmap (\ !x -> (getField 1 sep x, fastaSeq x)) + +-- | Get a mapping from accession to if the cigar has all matching. +getMatchMap :: [BamRow] -> MatchMap +getMatchMap = MatchMap + . Map.fromListWith (&&) + . fmap (\ (BamRow !x) -> (x `at` 2, isIgnore $ x `at` 5)) + +-- | Better lookup error message. +lookupErr :: (Ord k, Show k) => k -> Map.Map k a -> a +lookupErr k = fromMaybe (error $ "Cannot find: " <> (show k)) . Map.lookup k + +-- | Better nub. +nub' :: (Eq a, Ord a) => [a] -> [a] +nub' = Set.toList . Set.fromList + +-- | Decode a SAM flag into the bit representation (as a string). +decodeSAMFlag :: Int -> String +decodeSAMFlag x = showIntAtBase 2 intToDigit x ""