modify-fasta (empty) → 0.8.0.0
raw patch · 4 files changed
+1003/−0 lines, 4 filesdep +basedep +containersdep +fastasetup-changed
Dependencies added: base, containers, fasta, mtl, optparse-applicative, pipes, pipes-text, regex-tdfa, regex-tdfa-text, split, text, text-show
Files
- LICENSE +339/−0
- Setup.hs +2/−0
- modify-fasta.cabal +37/−0
- src/Main.hs +625/−0
+ LICENSE view
@@ -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.) You can apply it to+your programs, too.++ When we speak of free software, we are referring to freedom, not+price. 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+ Setup.hs view
@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain
+ modify-fasta.cabal view
@@ -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
+ src/Main.hs view
@@ -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" )