TaxonomyTools (empty) → 1.0.0
raw patch · 8 files changed
+1122/−0 lines, 8 filesdep +EntrezHTTPdep +Taxonomydep +aesonsetup-changed
Dependencies added: EntrezHTTP, Taxonomy, aeson, base, bytestring, cassava, cmdargs, directory, either-unwrap, fgl, hxt, parsec, process, vector
Files
- LICENSE +675/−0
- Setup.hs +2/−0
- TaxonomyTools.cabal +87/−0
- src/Bio/Accessions2TaxIds.hs +110/−0
- src/Bio/TaxIds2Text.hs +55/−0
- src/Bio/TaxIds2Tree.hs +97/−0
- src/Bio/TaxIds2TreeCompare.hs +61/−0
- src/Bio/TaxIdsDistance.hs +35/−0
+ LICENSE view
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+ Setup.hs view
@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain
+ TaxonomyTools.cabal view
@@ -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 <ftp://ftp.ncbi.nih.gov/pub/taxonomy/ NCBI taxonomy dump> as input,+ .+ while other retrieve the data directly from the <http://www.ncbi.nlm.nih.gov/gquery/ NCBI Entrez REST> interface.+ .+ It is planned to support both datasources with each tool.+ .+ Usage instructions can be found in the <https://github.com/eggzilla/TaxonomyTools README>+ .+ 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
+ src/Bio/Accessions2TaxIds.hs view
@@ -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 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<!DOCTYPE eSearchResult PUBLIC \"-//NLM//DTD esearch 20060628//EN\" \"http://eutils.ncbi.nlm.nih.gov/eutils/dtd/20060628/esearch.dtd\">\n"+ string "<eSearchResult><Count>"+ many1 digit+ string "</Count><RetMax>"+ many1 digit + string "</RetMax><RetStart>"+ many1 digit+ string "</RetStart><IdList>\n"+ gis <- many1 (Text.ParserCombinators.Parsec.try parseGI)+ string "</IdList><TranslationSet/><QueryTranslation/></eSearchResult>"+ return gis++parseGI :: GenParser Char st Int+parseGI = do+ string "<Id>"+ gi <- many1 digit+ string "</Id>\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))+
+ src/Bio/TaxIds2Text.hs view
@@ -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
+ src/Bio/TaxIds2Tree.hs view
@@ -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
+ src/Bio/TaxIds2TreeCompare.hs view
@@ -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 [[]]+
+ src/Bio/TaxIdsDistance.hs view
@@ -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)