diff --git a/LICENSE b/LICENSE new file mode 100644 --- /dev/null +++ b/LICENSE @@ -0,0 +1,339 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. By contrast, the GNU General Public +License is intended to guarantee your freedom to share and change free +software--to make sure the software is free for all its users. This +General Public License applies to most of the Free Software +Foundation's software and to any other program whose authors commit to +using it. (Some other Free Software Foundation software is covered by +the GNU Lesser General Public License instead.) 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It is safest +to attach them to the start of each source file to most effectively +convey the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + 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 2 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, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + +Also add information on how to contact you by electronic and paper mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: + + Gnomovision version 69, Copyright (C) year name of author + Gnomovision 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, the commands you use may +be called something other than `show w' and `show c'; they could even be +mouse-clicks or menu items--whatever suits your program. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the program + `Gnomovision' (which makes passes at compilers) written by James Hacker. + + , 1 April 1989 + Ty Coon, President of Vice + +This 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. 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/modify-fasta.cabal b/modify-fasta.cabal new file mode 100644 --- /dev/null +++ b/modify-fasta.cabal @@ -0,0 +1,37 @@ +-- Initial modify-fasta.cabal generated by cabal init. For further +-- documentation, see http://haskell.org/cabal/users-guide/ + +name: modify-fasta +version: 0.8.0.0 +synopsis: Modify fasta (and CLIP) files in several optional ways +-- description: +homepage: https://github.com/GregorySchwartz/modify-fasta +license: GPL-2 +license-file: LICENSE +author: GregorySchwartz +maintainer: gregory.schwartz@drexel.edu +-- copyright: +category: Bioinformatics +build-type: Simple +cabal-version: >=1.8 + +executable modify-fasta + main-is: Main.hs + -- other-modules: + build-depends: base >=4.6 && <5 + , containers >=0.5 + , mtl >=2.1 + , text + , text-show + , split >=0.2 + , optparse-applicative >=0.11 + , fasta + , regex-tdfa >=1.2 + , regex-tdfa-text + , pipes >= 4.1 + , pipes-text + + -- Directories containing source files. + hs-source-dirs: src + + ghc-options: -O2 diff --git a/src/Main.hs b/src/Main.hs new file mode 100644 --- /dev/null +++ b/src/Main.hs @@ -0,0 +1,625 @@ +-- modify-fasta +-- By Gregory W. Schwartz + +-- Takes a fasta file filters the fasta file in several ways. + +{-# LANGUAGE BangPatterns #-} + +-- Built-in +import Data.Maybe +import qualified Data.Map as M +import qualified System.IO as IO +import qualified Data.Text.IO as IO +import Control.Monad + +-- Cabal +import qualified Data.Text as T +import qualified Data.Text.IO as T +import Options.Applicative +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 Data.List.Split as Split + +-- Local +import Types +import Utility +import FilterCloneMap +import FilterFastaList +import FilterCloneList +import TransformFastaList +import TransformCloneList +import Print + +-- Command line arguments +data Options = Options { input :: String + , aminoAcidsFlag :: String + , legacyFlag :: Bool + , clipFastaFlag :: Bool + , convertToAminoAcidsFlag :: Bool + , inputFillIn :: FillInValue + , inputStart :: Maybe Int + , inputStop :: Maybe Int + , inputMinSequenceMutation :: Maybe Int + , inputMutationCount :: Maybe Int + , inputMutationPercent :: Maybe Double + , addLengthFlag :: Bool + , removeTheNsFlag :: Bool + , removeGermlinesPreFlag :: Bool + , removeHighlyMutatedFlag :: Bool + , removeStopsFlag :: Bool + , removeDuplicatesFlag :: Bool + , removeOutOfFrameFlag :: Bool + , removeUnknownNuc :: Bool + , inputInFrame :: Maybe Field + , inputOutFrame :: Maybe Field + , trimFrame :: Bool + , inputStopRange :: Int + , inputCodonMut :: CodonMut + , inputCodonMutType :: String + , inputMutType :: String + , inputChangeField :: String + , inputCustomFilter :: String + , customGermlineFlag :: Bool + , customRemoveFlag :: Bool + , inputGeneAlleleField :: Int + , countFlag :: Bool + , output :: String + } + +-- Command line options +options :: Parser Options +options = Options + <$> strOption + ( long "input" + <> short 'i' + <> metavar "FILE" + <> value "" + <> help "The input fasta file or CLIP fasta file" ) + <*> strOption + ( long "unit" + <> short 'u' + <> metavar "AminoAcid|Nucleotide" + <> help "Whether these sequences are composed of\ + \ amino acids (AminoAcid) or nucleotides (Nucleotide)" ) + <*> switch + ( long "legacy" + <> short 'L' + <> help "Whether to use the legacy version with no pipes. Note: The\ + \ legacy version supports more features but is greedy\ + \ in terms of speed and memory. Use only if really needed.\ + \ Features that are legacy only are noted in this\ + \ documentation" ) + <*> switch + ( long "clip-fasta" + <> short 'A' + <> help "Whether the input is a clip fasta file (has germline >>\ + \ sequences)." ) + <*> switch + ( long "convert-to-amino-acids" + <> short 'C' + <> help "Whether to convert the filtered sequences to amino acids\ + \ in the output. Applied last, even after add length." ) + <*> option auto + ( long "fill-in" + <> short 'F' + <> metavar "(FIELD, START, 'CHARACTER')" + <> value (-1, -1, 'X') + <> help "Use the FIELD index (1 indexed, split by '|') in the\ + \ header to fill in the unknown character CHARACTER with the\ + \ respective character in that field. Use the START value\ + \ to let the program know where the string in the field starts\ + \ from in the sequence. For instance, a header of >H2O|HELLO\ + \ for the sequence HIMANHELXODUDE and a value of fill-in of\ + \ (2, 6, 'X') would change the sequence to HIMANHELLODUDE. If\ + \ the string in the field has the unknown character as well,\ + \ i.e. >H2O|HELXO, then the sequence is considered bad and is\ + \ removed" ) + <*> optional ( option auto + ( long "start" + <> short 't' + <> metavar "[ ] | INT" + <> help "Remove everything before this position (1 indexed).\ + \ Done first just after filtering." ) ) + <*> optional ( option auto + ( long "stop" + <> short 'p' + <> metavar "[ ] | INT" + <> help "Remove everything after this position (1 indexed).\ + \ Done first just after filtering." ) ) + <*> optional ( option auto + ( long "frequent-mutation-min" + <> metavar "[ ] | INT" + <> help "Minimum number of sequences required for a clone to be valid\ + \ in the calculation of frequent mutations, replaces\ + \ with gaps otherwise" ) ) + <*> optional ( option auto + ( long "frequent-mutation-count" + <> metavar "[ ] | INT" + <> help "Only include codons containing a mutation present in this\ + \ many sequences in the clone or more. 0 is all sequences.\ + \ Converts the unincluded codons to gaps." ) ) + <*> optional ( option auto + ( long "frequent-mutation-percent" + <> metavar "[ ] | PERCENT" + <> help "Only include codons containing a mutation present in this\ + \ percentage of sequences in the clone or more.\ + \ 0 is all sequences. Converts the unincluded codons\ + \ to gaps." ) ) + <*> switch + ( long "add-length" + <> short 'l' + <> help "Whether to append the length of the sequence to the end of\ + \ the header, calculated after --convert-to-amino-acids\ + \ if enabled" ) + <*> switch + ( long "remove-N" + <> short 'N' + <> help "Whether to replace N or n in the sequence with a gap, '-'" ) + <*> switch + ( long "remove-germlines" + <> short 'g' + <> help "Whether to remove germlines." ) + <*> switch + ( long "remove-highly-mutated" + <> short 'h' + <> help "Whether to remove highly mutated clone sequences (a third\ + \ of their sequence are different amino acids)." ) + <*> switch + ( long "remove-stops" + <> short 's' + <> help "Whether to remove sequences with stop codons" ) + <*> switch + ( long "legacy-remove-duplicates" + <> short 'd' + <> help "Whether to remove duplicate sequences. LEGACY ONLY" ) + <*> switch + ( long "remove-out-of-frame" + <> short 'O' + <> help "Whether to remove sequences that are out of frame--if the\ + \ sequences or number of gaps is not divisible by 3" ) + <*> switch + ( long "remove-unknown-nucleotides" + <> short 'Y' + <> help "Convert unknown nucleotides (not ACGTN-.) to gaps (-)" ) + <*> optional ( option auto + ( long "input-inframe" + <> metavar "[ ] | FIELD" + <> help "Represents the 1 indexed field split by '|'\ + \ containing the inframe\ + \ value (frames are 0, 1, or 2 like\ + \ USCS definitions). For use with trim-frame." ) + ) + <*> optional ( option auto + ( long "input-outframe" + <> metavar "[ ] | FIELD" + <> help "Represents the 1 indexed field split by '|'\ + \ containing the outframe\ + \ value (frames are 0, 1, or 2 like\ + \ USCS definitions). For use with trim-frame." ) + ) + <*> switch + ( long "trim-frame" + <> short 'y' + <> help "Trim each sequence to be in frame by remove extra nucleotides\ + \ at the end. If input-inframe or input-outframe is\ + \ specified, follow those rules instead." ) + <*> option auto + ( long "input-stop-range" + <> short 'r' + <> metavar "[106]|INT" + <> value 106 + <> help "Only search for stops with remove-stops up to this\ + \ amino acid position" ) + <*> option auto + ( long "input-codon-mut" + <> short 'c' + <> metavar "[-1]|0|1|2|3" + <> value (-1) + <> help "Only include codons with this many mutations or less or more,\ + \ depending on input-codon-mut-type (-1 is the same as include\ + \ all codons). Converts the unincluded codon to gaps." ) + <*> strOption + ( long "input-codon-mut-type" + <> short 'T' + <> metavar "[=]|>|<" + <> value "=" + <> help "Only include codons with this many mutations (=)\ + \ (or lesser (<) or greater (>), depending on\ + \ input-codon-mut). Converts the unincluded codon to gaps." ) + <*> strOption + ( long "input-mut-type" + <> short 'M' + <> metavar "[All]|Silent|Replacement" + <> value "All" + <> help "Only include codons with this all mutations (All),\ + \ (or silent (Silent) or replacement (Replacement))." ) + <*> strOption + ( long "input-change-field" + <> short 'e' + <> metavar "((FIELD (Int), VALUE (String))" + <> value "" + <> help "Change a field to a match, so a regex \"ch.*_\" to field 2\ + \ of \">abc|brie_cheese_dude\" would result in\ + \ \">abc|cheese_\". Useful for getting specific properties\ + \ from a field. Can take a list of format\ + \ \"(Int, String)&&(Int, String)&& ...\" and so on. The String\ + \ is in regex format (POSIX extended).\ + \ The first in the tuple is the location of the field\ + \ (1 indexed, split by '|')." ) + <*> strOption + ( long "input-custom-filter" + <> short 'f' + <> metavar "((FIELD (Int), VALUE (String))" + <> value "" + <> help "A custom filter. Can take a list of format\ + \ \"(Int, String)&&(Int, String)&& ...\" and so on. The String\ + \ is in regex format (POSIX extended), so if the entire\ + \ string 'a' is in the whole field, then you need to input\ + \ '^a$' for the beginning to the end!\ + \ The first in the tuple is the location of the field\ + \ (1 indexed, split by '|'). If you want to apply to\ + \ the entire header, either have the location as 0 or\ + \ exclude the location altogether (, Day 3|IGHV3) for instance\ + \ will match if the entire header is '>Day 3|IGHV3'.\ + \ This list will be filtered one at a time, so you cannot\ + \ get multiple filters, but you can remove multiple filters." ) + <*> switch + ( long "legacy-custom-germline" + <> short 'G' + <> help "Whether to apply the custom filter to germlines (>>)\ + \ instead of sequences (>). LEGACY ONLY" ) + <*> switch + ( long "custom-remove" + <> short 'm' + <> help "Whether to remove the sequences containing the custom filter\ + \ as opposed to remove the sequences that don't contain the\ + \ filter" ) + <*> option auto + ( long "legacy-gene-allele-field" + <> short 'V' + <> metavar "[1]|INT" + <> value 1 + <> help "The field (1 indexed) of the gene allele name. LEGACY ONLY" ) + <*> switch + ( long "legacy-count" + <> short 'v' + <> help "Do not save output, just count genes and alleles from\ + \ the results. Requires gene-allele-field. LEGACY ONLY" ) + <*> strOption + ( long "output" + <> short 'o' + <> metavar "FILE" + <> value "" + <> help "The output fasta file" ) + +-- | Parse the argument fieldInt +fieldIntParser :: String -> [(Maybe Int, T.Text)] +fieldIntParser "" = [] +fieldIntParser s = map (\x -> (first x, second x)) . Split.splitOn "&&" $ s + where + first x + | (head . Split.splitOn "," $ x) == "(" = Nothing + | otherwise = + Just (read (tail . head . Split.splitOn "," $ x) :: Int) + second = T.pack . init . dropWhile (== ' ') . last . Split.splitOn "," + +-- | Check for amino acid +isAminoAcid :: GeneticUnit -> Bool +isAminoAcid AminoAcid = True +isAminoAcid _ = False + +modifyFastaList :: Options -> IO () +modifyFastaList opts = do + hIn <- if null . input $ opts + then return IO.stdin + else IO.openFile (input opts) IO.ReadMode + hOut <- if null . output $ opts + then return IO.stdout + else IO.openFile (output opts) IO.WriteMode + let genUnit = read . aminoAcidsFlag $ opts + stopRange = inputStopRange opts + customFilters = fieldIntParser . inputCustomFilter $ opts + changeFields = fieldIntParser . inputChangeField $ opts + codonMut = inputCodonMut opts + codonMutType = T.pack . inputCodonMutType $ opts + mutType = T.pack . inputMutType $ opts + + -- Remove out of frame sequences + seqInFrame x = not ( removeOutOfFrameFlag opts + && (not . isAminoAcid $ genUnit) + ) + || isInFrame x + + -- Start filtering out sequences + -- Include only custom filter sequences + customFilter x = null customFilters + || hasAllCustomFilters + (customRemoveFlag opts) + customFilters + x + + -- Remove clones with stops in the range + noStops x = not (removeStopsFlag opts) || hasNoStops genUnit stopRange x + + -- Remove Ns from fasta list + noNs = if removeTheNsFlag opts && (not . isAminoAcid $ genUnit) + then removeN + else id + + -- Change fasta headers with match + changeHeader x = if not . null $ changeFields + then changeAllFields x changeFields + else x + + -- Get a specific region of the sequence + cutSequence = case (inputStart opts, inputStop opts) of + (Nothing, Nothing) -> id + (start, stop) -> getRegionSequence start stop + + -- Remove non standard nucleotides + removeUnknown = if removeUnknownNuc opts + then removeUnknownNucs + else id + + -- Trim sequence + trim fs = + if trimFrame opts + then trimFasta + genUnit + ((read . T.unpack . flip getField fs) <$> inputInFrame opts) + ((read . T.unpack . flip getField fs) <$> inputOutFrame opts) + fs + else fs + + -- Fill in bad characters at the requested section with possible + -- replacements + fillIn = case inputFillIn opts of + (-1, -1, 'X') -> id + (f, s, c) -> fillInSequence f s c + + -- Convert to amino acids + ntToaa = if convertToAminoAcidsFlag opts + then convertToAminoAcidsFastaSequence + else id + + -- Include sequence length in header at the end + includeLength = if addLengthFlag opts + then addLengthHeader + else id + + -- CLIP fasta specific filters and transformations + + -- Remove highly mutated sequences + removeHighMutations = if removeHighlyMutatedFlag opts + then filterHighlyMutatedEntry genUnit + else id + + -- Extract mutations to a certain degree + getMutations = if codonMut > -1 + then onlyMutations codonMut codonMutType mutType + else id + + -- Extract mutations to a certain degree + getFrequentMutations = if isJust (inputMutationCount opts) + || isJust (inputMutationPercent opts) + then frequentMutations + (inputMinSequenceMutation opts) + (inputMutationCount opts) + (inputMutationPercent opts) + else id + + -- Final order + filterOrder x = seqInFrame x && customFilter x && noStops x + transformOrder = includeLength + . ntToaa + . changeHeader + . removeUnknown + . trim + . noNs + . fillIn + . cutSequence + -- Specifically for germlines, as we don't want to change header or + -- fill in the germline because that would make no sense in this + -- case + transformGermline = includeLength + . ntToaa + . removeUnknown + . trim + . noNs + . cutSequence + -- Specifically for CLIP fasta files + transformOrderCLIP = getFrequentMutations + . getMutations + . removeHighMutations + + executePrintFasta x = mappend (showFasta x) (T.pack "\n") + executePrintCLIPFasta x = + mappend + (printCloneEntry (removeGermlinesPreFlag opts) x) + (T.pack "\n") + + -- Execute pipes + if clipFastaFlag opts + then + runEffect $ ( ( pipesCLIPFasta (PT.fromHandle hIn) + >-> P.map ( \(!germline, !fseqs) -> + (germline, filter filterOrder fseqs) + ) -- Filter sequences + >-> P.map transformOrderCLIP -- Transform specifically for CLIP fasta + >-> P.map ( \(!germline, !fseqs) -> + ( transformGermline germline + , map transformOrder fseqs + ) + ) -- Transform sequences, only do some for germline + >-> P.map ( \(!germline, !fs) + -> ( germline + , filter (not . T.null . fastaSeq) fs + ) + ) -- Remove empty sequences + >-> P.filter (not . null . snd) -- Remove empty clones + >-> P.map executePrintCLIPFasta ) -- Print the results + >> yield (T.pack "\n") ) -- want that newline at the end + >-> PT.toHandle hOut + else + runEffect $ ( ( pipesFasta (PT.fromHandle hIn) + >-> P.filter filterOrder -- Filter + >-> P.map transformOrder -- Transform + >-> P.filter (not . T.null . fastaSeq) -- Remove empty sequences + >-> P.map executePrintFasta ) -- Print the results + >> yield (T.pack "\n") ) -- want that newline at the end + >-> PT.toHandle hOut + + -- Finish up by closing file if written + unless (null . output $ opts) (IO.hClose hOut) + +-- Legacy function +modifyFastaCloneMap :: Options -> IO () +modifyFastaCloneMap opts = do + contents <- if null . input $ opts + then T.getContents + else T.readFile . input $ opts + -- No redundant newlines in sequence + let genUnit = read . aminoAcidsFlag $ opts + stopRange = inputStopRange opts + codonMut = inputCodonMut opts + codonMutType = T.pack . inputCodonMutType $ opts + mutType = T.pack . inputMutType $ opts + customFilters = fieldIntParser $ inputCustomFilter opts + removeGermlinesFlag = if not . clipFastaFlag $ opts + then True + else removeGermlinesPreFlag opts + + -- Initiate CloneMap + cloneMapFrames = if not . clipFastaFlag $ opts + then addFillerGermlines + . parsecFasta + $ contents + else parsecCLIPFasta contents + + -- Remove out of frame sequences + cloneMapInFrame = if (removeOutOfFrameFlag opts && ( not + . isAminoAcid + $ genUnit ) ) + then removeOutOfFrameSeqs cloneMapFrames + else cloneMapFrames + + -- Remove Ns from CloneMap + cloneMap = if (removeTheNsFlag opts && ( not + . isAminoAcid + $ genUnit ) ) + then removeCLIPNs cloneMapInFrame + else cloneMapInFrame + + -- Start filtering out sequences + -- Include only custom filter sequences + cloneMapCustom = if not . null $ customFilters + then removeAllCustomFilters + (customGermlineFlag opts) + (customRemoveFlag opts) + cloneMap + customFilters + else cloneMap + -- Remove clones with stops in the range + (cloneMapNoStops, errorString) = if removeStopsFlag opts + then removeStopsCloneMap + genUnit + stopRange + cloneMapCustom + else (cloneMapCustom, Nothing) + -- Output Error if necessary + case errorString of + Nothing -> return () + Just x -> error x + + -- Remove duplicate sequences + let cloneMapNoDuplicates = if removeDuplicatesFlag opts + then removeDuplicatesCloneMap + cloneMapNoStops + else cloneMapNoStops + + -- Remove clones that are highly mutated + (cloneMapLowMutation, errorString2) = if (removeHighlyMutatedFlag opts) + && ( not + . isAminoAcid + $ genUnit ) + then filterHighlyMutated + genUnit + cloneMapNoDuplicates + else ( cloneMapNoDuplicates + , Nothing ) + + -- Output Error if necessary + case errorString2 of + Nothing -> return () + Just x -> error x + + -- Remove codons with codons with a certain number of mutations + let cloneMapNoCodonMut = if codonMut > -1 + then removeCodonMutCount codonMut + codonMutType + mutType + cloneMapLowMutation + else cloneMapLowMutation + -- Remove empty clones + cloneMapNoEmptyClones = removeEmptyClone cloneMapNoCodonMut + + -- Convert sequences to amino acids + (cloneMapAA, errorString3) = if (convertToAminoAcidsFlag opts) + && (not . isAminoAcid $ genUnit) + then convertToAminoAcidsCloneMap + cloneMapNoEmptyClones + else (cloneMapNoEmptyClones, Nothing) + + -- Output Error if necessary + case errorString3 of + Nothing -> return () + Just x -> error x + + -- Break if there are no sequences to output + case M.null cloneMapAA of + True -> error "No sequences left! Nothing written." + False -> return () + + -- What to do with results + case countFlag opts of + True -> do + -- Print results + let outputText = printSequenceCount + (clipFastaFlag opts) + (inputGeneAlleleField opts) + cloneMapAA + -- Print results to stdout + T.putStrLn outputText + False -> do + -- Print results + let outputText = if removeGermlinesFlag + then printFastaNoGermline cloneMapAA + else printFasta cloneMapAA + + -- Save results + if null . output $ opts + then T.putStrLn outputText + else T.writeFile (output opts) outputText + +modifyFasta :: Options -> IO () +modifyFasta opts = if legacyFlag opts + then modifyFastaCloneMap opts + else modifyFastaList opts + +main :: IO () +main = execParser opts >>= modifyFasta + where + opts = info (helper <*> options) + ( fullDesc + <> progDesc "Modify fasta (and CLIP) files in several optional ways.\ + \ Order of transformation goes: seqInFrame -> customFilter\ + \ -> noStops -> removeHighMutations -> getMutations ->\ + \ getFrequentMutations -> cutSequence -> fillIn -> noNs\ + \ -> changeHeader -> ntToaa -> includeLength,\ + \ so if you require a different\ + \ order (which can change results dramatically), then do\ + \ so one at a time through the wonderful world of piping." + <> header "modify-fasta, Gregory W. Schwartz" )