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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: + + Copyright (C) + 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/TaxonomyTools.cabal b/TaxonomyTools.cabal new file mode 100644 --- /dev/null +++ b/TaxonomyTools.cabal @@ -0,0 +1,87 @@ +name: TaxonomyTools +-- The package version. See the Haskell package versioning policy (PVP) +-- for standards guiding when and how versions should be incremented. +-- http://www.haskell.org/haskellwiki/Package_versioning_policy +-- PVP summary: +-+------- breaking API changes +-- | | +----- non-breaking API additions +-- | | | +--- code changes with no API change +version: 1.0.0 +synopsis: Tool for parsing, processing, comparing and visualizing taxonomy data +description: Taxonomy Tool utilizes functions from the Taxonomy library to provide + . + several commandline utilities for routine-tasks with taxonomy data. + . + Currently some tools accept either the as input, + . + while other retrieve the data directly from the interface. + . + It is planned to support both datasources with each tool. + . + Usage instructions can be found in the + . + Currently following Tools are included: + . + * Accessions2TaxIds: + Converts a list of NCBI accession numbers into NCBI taxonomy ids + . + * TaxIds2Tree: + List of taxonomy ids is converted into a graphical tree representation + either as .svg (via graphviz) or as .json (via d3js). + . + * TaxIds2TreeCompare: + Multiple lists of taxonomy ids are converted into a visualisation of the + taxonomic tree highlighting the input nodes corresponding to their list. + . + * TaxIds2Text: + List of taxonomy ids is converted in a short text summary for each node. + . + * TreeDistance: + Computes the distance between two input nodes on the given tree. + +license: GPL-3 +license-file: LICENSE +author: Florian Eggenhofer +maintainer: egg@tbi.univie.ac.at +-- copyright: +category: Bioinformatics +build-type: Simple +cabal-version: >=1.8 + +source-repository head + type: git + location: https://github.com/eggzilla/TaxonomyTools + +source-repository this + type: git + location: https://github.com/eggzilla/TaxonomyTools/tree/1.0.0 + tag: 1.0.0 + +executable TaxIds2Text + Hs-Source-Dirs: ./src/Bio/ + main-is: TaxIds2Text.hs + ghc-options: -Wall -O2 + build-depends: base >=4.5 && <5, cmdargs, Taxonomy, either-unwrap, fgl, bytestring + +executable Accessions2TaxIds + Hs-Source-Dirs: ./src/Bio/ + main-is: Accessions2TaxIds.hs + ghc-options: -Wall -O2 -fno-warn-unused-do-bind + build-depends: base >=4.5 && <5, cmdargs, process, directory, Taxonomy, either-unwrap, fgl, cassava, vector, bytestring, parsec, EntrezHTTP, hxt + +executable TaxIds2TreeCompare + Hs-Source-Dirs: ./src/Bio/ + main-is: TaxIds2TreeCompare.hs + ghc-options: -Wall -O2 + build-depends: base >=4.5 && <5, cmdargs, process, directory, Taxonomy, either-unwrap, fgl, cassava, vector, bytestring + +executable TaxIds2Tree + Hs-Source-Dirs: ./src/Bio/ + main-is: TaxIds2Tree.hs + ghc-options: -Wall -O2 + build-depends: base >=4.5 && <5, cmdargs, process, directory, Taxonomy, either-unwrap, fgl, cassava, vector, bytestring, aeson + +executable TaxIdsDistance + Hs-Source-Dirs: ./src/Bio/ + main-is: TaxIdsDistance.hs + ghc-options: -Wall -O2 + build-depends: base >=4.5 && <5, cmdargs, process, directory, Taxonomy, either-unwrap, fgl, vector, bytestring diff --git a/src/Bio/Accessions2TaxIds.hs b/src/Bio/Accessions2TaxIds.hs new file mode 100644 --- /dev/null +++ b/src/Bio/Accessions2TaxIds.hs @@ -0,0 +1,110 @@ +{-# LANGUAGE RecordWildCards #-} +{-# LANGUAGE DeriveDataTypeable #-} +{-# LANGUAGE Arrows #-} + +--dist/build/Accessions2TaxIds/Accessions2TaxIds -i /scratch/egg/AccessionList > ~egg/TaxidOut + +module Main where + +import System.Console.CmdArgs +import Text.ParserCombinators.Parsec +import Data.List +import Data.Either.Unwrap +import Control.Concurrent +import Bio.EntrezHTTP +import Text.XML.HXT.Core + +data Options = Options + { inputFilePath :: String + } deriving (Show,Data,Typeable) + +options :: Options +options = Options + { inputFilePath = def &= name "i" &= help "Path to input accession file containing taxids seperated by linebreaks." + } &= summary "Accessions2TaxIds" &= help "Florian Eggenhofer - 2015" &= verbosity + +main :: IO [()] +main = do + Options{..} <- cmdArgs options + accessionsFile <- readFile inputFilePath + let accessions = lines accessionsFile + gis <- retrieveGIsEntrez accessions + taxIds <- retrieveTaxIdsEntrez gis + mapM putStrLn (map show taxIds) + + +retrieveTaxIdsEntrez :: [Int] -> IO [Int] +retrieveTaxIdsEntrez geneIds = do + taxIdsOutput <- retrieveElementsEntrez geneIds retrieveTaxIdEntrez + let taxids = concatMap readEntrezTaxId taxIdsOutput + return taxids + +retrieveGIsEntrez :: [String] -> IO [Int] +retrieveGIsEntrez accessions = do + gisOutput <- retrieveElementsEntrez accessions retrieveGIEntrez + let parsedGisOutput = map parseGIfromEntrez gisOutput + let gis = concatMap fromRight parsedGisOutput + return gis + +retrieveGIEntrez :: [String] -> IO String +retrieveGIEntrez accessions = do + let idList = intercalate "," accessions + let query' = "retmax=400&term=" ++ idList + let entrezQuery = EntrezHTTPQuery (Just "esearch") (Just "nucleotide") query' + threadDelay 10000000 + result <- entrezHTTP entrezQuery + return result + +parseGIfromEntrez :: String -> Either ParseError [Int] +parseGIfromEntrez input = parse genParserGIfromEntrez "genParserGIfromEntrez" input + +genParserGIfromEntrez :: GenParser Char st [Int] +genParserGIfromEntrez = do + string "\n\n" + string "" + many1 digit + string "" + many1 digit + string "" + many1 digit + string "\n" + gis <- many1 (Text.ParserCombinators.Parsec.try parseGI) + string "" + return gis + +parseGI :: GenParser Char st Int +parseGI = do + string "" + gi <- many1 digit + string "\n" + return (readInt gi) + +retrieveTaxIdEntrez :: [Int] -> IO String +retrieveTaxIdEntrez geneIds = do + let geneIdStrings = map show geneIds + let idList = intercalate "," geneIdStrings + let query' = "id=" ++ idList + let entrezQuery = EntrezHTTPQuery (Just "esummary") (Just "nucleotide") query' + threadDelay 10000000 + result <- entrezHTTP entrezQuery + return result + +readEntrezTaxId :: String -> [Int] +readEntrezTaxId input = runLA (xreadDoc >>> getEntrezTaxId) input + +getEntrezTaxId :: ArrowXml a => a XmlTree Int +getEntrezTaxId = getChildren >>> atTag "DocSum" >>> + proc entrezDocSum -> do + taxId <- atName "TaxId" >>> getChildren >>> getText -< entrezDocSum + returnA -< read taxId :: Int + +readInt :: String -> Int +readInt = read + +-- | gets all subtrees with the specified tag name +atTag :: ArrowXml a => String -> a XmlTree XmlTree +atTag tag = deep (isElem >>> hasName tag) + +atName :: ArrowXml a => String -> a XmlTree XmlTree +atName elementId = deep (isElem >>> hasAttrValue "Name" (== elementId)) + diff --git a/src/Bio/TaxIds2Text.hs b/src/Bio/TaxIds2Text.hs new file mode 100644 --- /dev/null +++ b/src/Bio/TaxIds2Text.hs @@ -0,0 +1,55 @@ +{-# LANGUAGE RecordWildCards #-} +{-# LANGUAGE DeriveDataTypeable #-} +{-# LANGUAGE Arrows #-} + +-- ./dist/build/TaxIds2Text/TaxIds2Text -t /home/mescalin/egg/current/Projects/Haskell/TaxonomyTools/RF00169_accessionnumbers.tax -r Phylum -i /scratch/egg/taxdmpnew/ > out.csv +module Main where + +import System.Console.CmdArgs +import Data.Either.Unwrap +import qualified Data.ByteString.Char8 as BC +import Bio.Taxonomy +import Data.Maybe +import Text.Read + +data Options = Options + { taxDumpDirectoryPath :: String, + taxonomicRank :: String, + taxNodeListFilePath :: String + } deriving (Show,Data,Typeable) + +options :: Options +options = Options + { taxDumpDirectoryPath = def &= name "i" &= help "Path to input NCBI taxonomy dump files directory", + taxonomicRank = "Class" &= name "r" &= help "Requested taxonomic rank - default Class", + taxNodeListFilePath = def &= name "t" &= help "Path to input taxonomy id list without header" + } &= summary "TaxIds2Text - List of taxonomy ids is converted in a short text summary for each node." &= help "Florian Eggenhofer - 2015" &= verbosity + +main :: IO () +main = do + Options{..} <- cmdArgs options + graphOutput <- readNamedTaxonomy taxDumpDirectoryPath + let currentRank = readMaybeRank taxonomicRank + if isNothing currentRank + then putStrLn "Please provide a valid taxonomic Rank (e.g. Class)." + else do + if isLeft graphOutput + then print ("Could not parse provided taxonomy dump files" ++ show (fromLeft graphOutput)) + else do + if null taxNodeListFilePath + then do + putStrLn "Provide a path to input taxonomy id list or to RNAlienResult CSV." + else do -- input taxid path present + taxidtable <- readFile taxNodeListFilePath + let taxidtableentries = map (\l -> read l :: Int) (lines taxidtable) + let graph = fromRight graphOutput + let maybeParentNodes = map (\taxidtableentry -> getParentbyRank taxidtableentry graph (Just Phylum)) taxidtableentries + let parentNodeStrings = map (\maybeParentNode -> maybe "not found,not found" (\(_,n) -> printSimpleNode n) maybeParentNode) maybeParentNodes + let outputCSV = map (\(txid,parentNodeString) -> (show txid) ++ "," ++ parentNodeString) (zip taxidtableentries parentNodeStrings) + mapM_ putStrLn outputCSV + +printSimpleNode :: SimpleTaxon -> String +printSimpleNode snode = show (simpleRank snode) ++ "," ++ BC.unpack (simpleScientificName snode) + +readMaybeRank :: String -> Maybe Rank +readMaybeRank inputString = readMaybe inputString diff --git a/src/Bio/TaxIds2Tree.hs b/src/Bio/TaxIds2Tree.hs new file mode 100644 --- /dev/null +++ b/src/Bio/TaxIds2Tree.hs @@ -0,0 +1,97 @@ +{-# LANGUAGE RecordWildCards #-} +{-# LANGUAGE DeriveDataTypeable #-} +-- | TaxIds2Tree +-- dist/build/TaxIds2Tree/TaxIds2Tree -i /scratch/egg/data/taxdump/ -o /home/mescalin/egg/current/Projects/Haskell/TaxonomyTools/ -t /home/mescalin/egg/current/Projects/Haskell/TaxonomyTools/RF00169_accessionnumbers.tax -f json -l 4 +-- dot -Tsvg taxonomy.dot -o taxonomy.svg +module Main where + +import Prelude +import System.Console.CmdArgs +import Bio.Taxonomy +import Data.Either.Unwrap +import Data.Graph.Inductive +import Data.Csv +import qualified Data.Vector as V +import qualified Data.ByteString.Lazy.Char8 as L +import Data.Char +import qualified Data.Aeson.Encode as E +-------------------------------------------------------- + +data Options = Options + { taxDumpDirectoryPath :: String, + taxNodeListFilePath :: String, + alienCSVFilePath ::String, + levels :: Int, + outputFormat :: String, + outputDirectoryPath :: String + } deriving (Show,Data,Typeable) + +options :: Options +options = Options + { taxDumpDirectoryPath = def &= name "i" &= help "Path to input NCBI taxonomy dump files directory", + taxNodeListFilePath = def &= name "t" &= help "Path to input taxonomy id list without header", + alienCSVFilePath = def &= name "r" &= help "Path to RNAlienResult CSV. Alternative to input taxonomy id list", + levels = (1 ::Int) &= name "l" &= help "Number defining maximum distance from root for nodes in subtree.", + outputFormat = "dot" &= name "f" &= help "Requested output format (json,dot). Default: dot", + outputDirectoryPath = def &= name "o" &= help "Path to output directory" + } &= summary "TaxIds2Tree - List of taxonomy ids is converted into a graphical tree representation either as .svg (via graphviz) or as .json (via d3js)" &= help "Florian Eggenhofer - 2015" &= verbosity + +main :: IO () +main = do + Options{..} <- cmdArgs options + graphOutput <- readNamedTaxonomy taxDumpDirectoryPath + if isLeft graphOutput then + print ("Could not parse provided taxonomy dump files" ++ show (fromLeft graphOutput)) + else + do if null taxNodeListFilePath then + do if null alienCSVFilePath then + putStrLn "Provide a path to input taxonomy id list or to RNAlienResult CSV." + else + do -- input AlienCSV path present + taxidtableentries <- extractTaxidsAlienCSV alienCSVFilePath + let graph = fromRight graphOutput + let currentSubgraph = extractTaxonomySubTreebyLevel taxidtableentries graph (Just levels) + --let subdiagram = drawTaxonomy (grev currentSubgraph) + --writeFile (outputDirectoryPath ++ "taxonomy.dot") subdiagram + generateOutput outputFormat outputDirectoryPath currentSubgraph + else + do -- input taxid path present + taxidtable <- readFile taxNodeListFilePath + let taxidtableentries = map (\l -> read l :: Int) (lines taxidtable) + let graph = fromRight graphOutput + let currentSubgraph = extractTaxonomySubTreebyLevel taxidtableentries graph (Just levels) + --let subdiagram = drawTaxonomy (grev currentSubgraph) + --writeFile (outputDirectoryPath ++ "taxonomy.dot") subdiagram + generateOutput outputFormat outputDirectoryPath currentSubgraph + +-- | generate output +generateOutput :: String -> String -> Gr SimpleTaxon Double -> IO () +generateOutput requestedFormat outputDirectoryPath inputGraph = do + case requestedFormat of + "dot" -> generateDotOutput outputDirectoryPath inputGraph + "json" -> generateJsonOutput outputDirectoryPath inputGraph + _ -> generateDotOutput outputDirectoryPath inputGraph + + +generateDotOutput :: String -> Gr SimpleTaxon Double -> IO () +generateDotOutput outputDirectoryPath inputGraph = do + let diagram = drawTaxonomy (grev inputGraph) + writeFile (outputDirectoryPath ++ "taxonomy.dot") diagram + + +generateJsonOutput :: String -> Gr SimpleTaxon Double -> IO () +generateJsonOutput outputDirectoryPath inputGraph = do + let jsonOutput = E.encode (grev inputGraph) + L.writeFile (outputDirectoryPath ++ "taxonomy.json") jsonOutput + + +-- | Extract taxids from RNAlien result.csv +extractTaxidsAlienCSV :: String -> IO [Node] +extractTaxidsAlienCSV alienCSVPath = do + let myOptions = defaultDecodeOptions { + decDelimiter = fromIntegral (ord ';') + } + inputCSV <- L.readFile alienCSVPath + let decodedCsvOutput = V.toList (fromRight (decodeWith myOptions HasHeader inputCSV :: Either String (V.Vector (Int,L.ByteString,L.ByteString)))) + let taxnodes = map (\(a,_,_) -> a :: Node) decodedCsvOutput + return taxnodes diff --git a/src/Bio/TaxIds2TreeCompare.hs b/src/Bio/TaxIds2TreeCompare.hs new file mode 100644 --- /dev/null +++ b/src/Bio/TaxIds2TreeCompare.hs @@ -0,0 +1,61 @@ +{-# LANGUAGE RecordWildCards #-} +{-# LANGUAGE DeriveDataTypeable #-} +-- | TaxIds2TreeCompare +-- dist/build/TaxIds2TreeCompare/TaxIds2TreeCompare -i /scratch/egg/taxdmpnew/ -l 4 -t /home/mescalin/egg/current/Projects/Haskell/TaxonomyTools/input.csv -o /home/mescalin/egg/current/Projects/Haskell/TaxonomyTools/ +-- dot -Tsvg comparison.dot -o comparison.svg +module Main where + +import Prelude +import System.Console.CmdArgs +import Bio.Taxonomy +import Data.Either.Unwrap +import Data.Graph.Inductive +import Data.Csv +import qualified Data.Vector as V +import qualified Data.ByteString.Lazy.Char8 as L +import Data.Char +-------------------------------------------------------- + +data Options = Options + { taxDumpDirectoryPath :: String, + taxNodeCSVFilePath :: String, + levels :: Int, + outputDirectoryPath :: String + } deriving (Show,Data,Typeable) + +options :: Options +options = Options + { taxDumpDirectoryPath = def &= name "i" &= help "Path to input NCBI taxonomy dump files directory", + taxNodeCSVFilePath = def &= name "t" &= help "Path to input taxonomy csv, each column with comma separated taxids represents one tree", + levels = (1 ::Int) &= name "l" &= help "Number defining maximum distance from root for nodes in subtree.", + outputDirectoryPath = def &= name "o" &= help "Path to output directory" + } &= summary "TaxIds2TreeCompare - Multiple lists of taxonomy ids are converted into a visualisation of the taxonomic tree highlighting the input nodes corresponding to their list." &= help "Florian Eggenhofer - 2015" &= verbosity + +main :: IO () +main = do + Options{..} <- cmdArgs options + graphOutput <- readNamedTaxonomy taxDumpDirectoryPath + if (isLeft graphOutput) + then do + print ("Could not parse provided taxonomy dump files" ++ show (fromLeft graphOutput)) + else do + let graph = fromRight graphOutput + treesTaxids <- extractTreesTaxidsCSV taxNodeCSVFilePath + let subgraphs = map (\treeTaxids -> extractTaxonomySubTreebyLevel treeTaxids graph (Just levels)) treesTaxids + let comparisonGraph = compareSubTrees subgraphs + let treeComparison = drawTreeComparison comparisonGraph + writeFile (outputDirectoryPath ++ "comparison.dot") treeComparison + +-- | Extract taxids from RNAlien result.csv +extractTreesTaxidsCSV :: String -> IO [[Node]] +extractTreesTaxidsCSV treesCSVPath = do + let myOptions = defaultDecodeOptions { + decDelimiter = fromIntegral (ord ',') + } + inputCSV <- L.readFile treesCSVPath + let decodedCsvOutput = V.toList (fromRight (decodeWith myOptions NoHeader inputCSV :: Either String (V.Vector ([Int])))) + --print (fromLeft (decodeWith myOptions NoHeader inputCSV :: Either String (V.Vector ([Int])))) + let treesTaxids = decodedCsvOutput + return treesTaxids + --return [[]] + diff --git a/src/Bio/TaxIdsDistance.hs b/src/Bio/TaxIdsDistance.hs new file mode 100644 --- /dev/null +++ b/src/Bio/TaxIdsDistance.hs @@ -0,0 +1,35 @@ +{-# LANGUAGE RecordWildCards #-} +{-# LANGUAGE DeriveDataTypeable #-} +-- | TaxonomyTools +-- dist/build/TaxIdsDistance/TaxIdsDistance -i /scratch/egg/data/taxdump/ -a 9986 -b 4039 +module Main where + +import Prelude +import System.Console.CmdArgs +import Bio.Taxonomy +import Data.Either.Unwrap +import Data.Graph.Inductive +-------------------------------------------------------- + +data Options = Options + { taxDumpDirectoryPath :: String, + organism1 :: Int, + organism2 :: Int + } deriving (Show,Data,Typeable) + +options :: Options +options = Options + { taxDumpDirectoryPath = def &= name "i" &= help "Path to input NCBI taxonomy dump files directory", + organism1 = def &= name "a" &= help "NCBI Taxonomy Id of the first organism", + organism2 = def &= name "b" &= help "NCBI Taxonomy Id of the second organism" + } &= summary "TaxIdsDistance - Computes the distance between two input nodes on the given tree." &= help "Florian Eggenhofer - 2015" &= verbosity + +main :: IO () +main = do + Options{..} <- cmdArgs options + graphOutput <- readNamedTaxonomy taxDumpDirectoryPath + if isLeft graphOutput then + print ("Could not parse provided taxonomy dump files" ++ show (fromLeft graphOutput)) + else + do let distance = sp (organism1 :: Node) (organism2 :: Node) (undir (fromRight graphOutput)) + print (length distance)