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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/Taxonomy.cabal b/Taxonomy.cabal new file mode 100644 --- /dev/null +++ b/Taxonomy.cabal @@ -0,0 +1,58 @@ +name: Taxonomy +-- 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: 1.0.1 +synopsis: Libary for parsing, processing and vizualization of taxonomy data +description: Haskell cabal Taxonomy libary contains tools, parsers, datastructures and visualisation + for the NCBI (National Center for Biotechnology Information) Taxonomy datasources. + . + It can utilize information from the REST interface via , + as well as from the files of the Taxonomy database . + . + Input data is parsed into a FGL based datastructure, which enables a wealth of processing + steps like node distances, retrieval of parent nodes or extraction of + subtrees. + . + Trees can be visualised via dot-format () + . + <> + . + or via json-format (). + . + The package contains tools based on this package. + +license: GPL-3 +license-file: LICENSE +author: Florian Eggenhofer +maintainer: florian.eggenhofer@univie.ac.at +-- copyright: +category: Bioinformatics +build-type: Simple +cabal-version: >=1.8 + +source-repository head + type: git + location: https://github.com/eggzilla/Taxonomy + +source-repository this + type: git + location: https://github.com/eggzilla/Taxonomy/tree/v1.0.1 + tag: v1.0.1 + +library + -- Modules exported by the library. + exposed-modules: Bio.TaxonomyData, Bio.Taxonomy + + -- compiler-options: + ghc-options: -Wall -O2 -fno-warn-unused-do-bind + + -- Other library packages from which modules are imported. + build-depends: base >=4.5 && <5, parsec, either-unwrap, fgl, text, graphviz, bytestring, aeson, vector + + -- Directories containing source files. + hs-source-dirs: src + diff --git a/src/Bio/Taxonomy.hs b/src/Bio/Taxonomy.hs new file mode 100644 --- /dev/null +++ b/src/Bio/Taxonomy.hs @@ -0,0 +1,583 @@ +-- | Functions for parsing, processing and visualization of taxonomy data. +-- +-- === Usage example: +-- * Read in taxonomy data +-- +-- > eitherTaxtree <- readNamedTaxonomy "/path/to/NCBI_taxonomydump_directory" +-- +-- * Process data +-- +-- > let subtree = extractTaxonomySubTreebyLevel [562] (fromRight eitherTaxTree) (Just 4) +-- +-- * Visualize result +-- +-- tput "/path/to/dotdirectory" subtree +module Bio.Taxonomy ( -- * Datatypes + -- Datatypes used to represent taxonomy data + module Bio.TaxonomyData, + -- * Parsing + -- Functions prefixed with "read" read from filepaths, functions with parse from Haskell Strings. + readTaxonomy, + readNamedTaxonomy, + parseTaxonomy, + parseNCBITaxCitations, + readNCBITaxCitations, + parseNCBITaxDelNodes, + readNCBITaxDelNodes, + parseNCBITaxDivisions, + readNCBITaxDivisions, + parseNCBITaxGenCodes, + readNCBITaxGenCodes, + parseNCBITaxMergedNodes, + readNCBITaxMergedNodes, + parseNCBITaxNames, + readNCBITaxNames, + parseNCBITaxNodes, + readNCBITaxNodes, + parseNCBISimpleTaxons, + readNCBISimpleTaxons, + readNCBITaxonomyDatabase, + -- * Processing + compareSubTrees, + extractTaxonomySubTreebyLevel, + extractTaxonomySubTreebyRank, + safeNodePath, + getParentbyRank, + -- * Visualization + drawTreeComparison, + drawTaxonomy, + writeTree, + writeDotTree, + writeJsonTree + ) where +import Prelude +import System.IO +import Bio.TaxonomyData +import Text.Parsec.Prim (runP) +import Text.ParserCombinators.Parsec +import Control.Monad +import Data.List +import qualified Data.Vector as V +import Data.Maybe +import qualified Data.Either.Unwrap as E +import Data.Graph.Inductive +import qualified Data.GraphViz as GV +import qualified Data.GraphViz.Printing as GVP +import qualified Data.GraphViz.Attributes.Colors as GVAC +import qualified Data.GraphViz.Attributes.Complete as GVA +import qualified Data.Text.Lazy as TL +import qualified Data.ByteString.Char8 as B +import qualified Data.ByteString.Lazy.Char8 as L +import qualified Data.Aeson.Encode as AE +-------------------------------------------------------- + +--------------------------------------- +-- Parsing functions + +-- | NCBI taxonomy dump nodes and names in the input directory path are parsed and a SimpleTaxon tree with scientific names for each node is generated. +readNamedTaxonomy :: String -> IO (Either ParseError (Gr SimpleTaxon Double)) +readNamedTaxonomy directoryPath = do + nodeNames <- readNCBITaxNames (directoryPath ++ "names.dmp") + let scientificNameBS = B.pack "scientific name" + if E.isLeft nodeNames + then return (Left (E.fromLeft nodeNames)) + else do + let nodeNamesVector = V.fromList (E.fromRight nodeNames) + let filteredNodeNames = V.filter (\a -> nameClass a == scientificNameBS) nodeNamesVector + parseFromFileEncISO88591 (genParserNamedTaxonomyGraph filteredNodeNames) (directoryPath ++ "nodes.dmp") + +-- | NCBI taxonomy dump nodes and names in the input directory path are parsed and a SimpleTaxon tree is generated. +readTaxonomy :: String -> IO (Either ParseError (Gr SimpleTaxon Double)) +readTaxonomy = parseFromFileEncISO88591 genParserTaxonomyGraph + +-- | NCBI taxonomy dump nodes and names in the input directory path are parsed and a SimpleTaxon tree is generated. +parseTaxonomy :: String -> Either ParseError (Gr SimpleTaxon Double) +parseTaxonomy = parse genParserTaxonomyGraph "parseTaxonomy" + +genParserTaxonomyGraph :: GenParser Char st (Gr SimpleTaxon Double) +genParserTaxonomyGraph = do + nodesEdges <- many1 (try genParserGraphNodeEdge) + optional eof + let (nodesList,edgesList) = unzip nodesEdges + let taxedges = filter (\(a,b,_) -> a /= b) edgesList + --let taxnodes = concat nodesList + --return (mkGraph taxnodes taxedges) + return $! mkGraph nodesList taxedges + +genParserNamedTaxonomyGraph :: V.Vector TaxName -> GenParser Char st (Gr SimpleTaxon Double) +genParserNamedTaxonomyGraph filteredNodeNames = do + nodesEdges <- many1 (try genParserGraphNodeEdge) + optional eof + let (nodesList,edgesList) = unzip nodesEdges + let taxedges = filter (\(a,b,_) -> a /= b) edgesList + let taxnamednodes = map (setNodeScientificName filteredNodeNames) nodesList + return $! mkGraph taxnamednodes taxedges + +setNodeScientificName :: V.Vector TaxName -> (t, SimpleTaxon) -> (t, SimpleTaxon) +setNodeScientificName inputTaxNames (inputNode,inputTaxon) = outputNode + where maybeRetrievedName = V.find (\a -> nameTaxId a == simpleTaxId inputTaxon) inputTaxNames + retrievedName = maybe (B.pack "no name") nameTxt maybeRetrievedName + outputNode = (inputNode,inputTaxon{simpleScientificName = retrievedName}) + +genParserGraphNodeEdge :: GenParser Char st ((Int,SimpleTaxon),(Int,Int,Double)) +genParserGraphNodeEdge = do + _simpleTaxId <- many1 digit + string "\t|\t" + _simpleParentTaxId <- many1 digit + string "\t|\t" + _simpleRank <- many1 (noneOf "\t") + many1 (noneOf "\n") + char '\n' + let _simpleTaxIdInt = readInt _simpleTaxId + let _simpleParentTaxIdInt = readInt _simpleParentTaxId + return ((_simpleTaxIdInt,SimpleTaxon _simpleTaxIdInt B.empty _simpleParentTaxIdInt (readRank _simpleRank)),(_simpleTaxIdInt,_simpleParentTaxIdInt,1 :: Double)) + +-- | parse NCBITaxCitations from input string +parseNCBITaxCitations :: String -> Either ParseError [TaxCitation] +parseNCBITaxCitations = parse genParserNCBITaxCitations "parseTaxCitations" + +-- | parse NCBITaxCitations from input filePath +readNCBITaxCitations :: String -> IO (Either ParseError [TaxCitation]) +readNCBITaxCitations = parseFromFileEncISO88591 genParserNCBITaxCitations + +-- | parse NCBITaxDelNodes from input string +parseNCBITaxDelNodes :: String -> Either ParseError [TaxDelNode] +parseNCBITaxDelNodes = parse genParserNCBITaxDelNodes "parseTaxDelNodes" + +-- | parse NCBITaxDelNodes from input filePath +readNCBITaxDelNodes :: String -> IO (Either ParseError [TaxDelNode]) +readNCBITaxDelNodes = parseFromFile genParserNCBITaxDelNodes + +-- | parse NCBITaxDivisons from input string +parseNCBITaxDivisions :: String -> Either ParseError [TaxDivision] +parseNCBITaxDivisions = parse genParserNCBITaxDivisons "parseTaxDivisons" + +-- | parse NCBITaxDivisons from input filePath +readNCBITaxDivisions :: String -> IO (Either ParseError [TaxDivision]) +readNCBITaxDivisions = parseFromFile genParserNCBITaxDivisons + +-- | parse NCBITaxGenCodes from input string +parseNCBITaxGenCodes :: String -> Either ParseError [TaxGenCode] +parseNCBITaxGenCodes = parse genParserNCBITaxGenCodes "parseTaxGenCodes" + +-- | parse NCBITaxGenCodes from input filePath +readNCBITaxGenCodes :: String -> IO (Either ParseError [TaxGenCode]) +readNCBITaxGenCodes = parseFromFile genParserNCBITaxGenCodes + +-- | parse NCBITaxMergedNodes from input string +parseNCBITaxMergedNodes :: String -> Either ParseError [TaxMergedNode] +parseNCBITaxMergedNodes = parse genParserNCBITaxMergedNodes "parseTaxMergedNodes" + +-- | parse NCBITaxMergedNodes from input filePath +readNCBITaxMergedNodes :: String -> IO (Either ParseError [TaxMergedNode]) +readNCBITaxMergedNodes = parseFromFile genParserNCBITaxMergedNodes + +-- | parse NCBITaxNames from input string +parseNCBITaxNames :: String -> Either ParseError [TaxName] +parseNCBITaxNames = parse genParserNCBITaxNames "parseTaxNames" + +-- | parse NCBITaxNames from input filePath +readNCBITaxNames :: String -> IO (Either ParseError [TaxName]) +readNCBITaxNames = parseFromFile genParserNCBITaxNames + +-- | parse NCBITaxNames from input string +parseNCBITaxNodes :: String -> Either ParseError TaxNode +parseNCBITaxNodes = parse genParserNCBITaxNode "parseTaxNode" + +-- | parse NCBITaxCitations from input filePath +readNCBITaxNodes :: String -> IO (Either ParseError [TaxNode]) +readNCBITaxNodes = parseFromFile genParserNCBITaxNodes + +-- | parse NCBISimpleTaxNames from input string +parseNCBISimpleTaxons :: String -> Either ParseError SimpleTaxon +parseNCBISimpleTaxons = parse genParserNCBISimpleTaxon "parseSimpleTaxon" + +-- | parse NCBITaxCitations from input filePath +readNCBISimpleTaxons :: String -> IO (Either ParseError [SimpleTaxon]) +readNCBISimpleTaxons = parseFromFile genParserNCBISimpleTaxons + +-- | Parse the input as NCBITax datatype +readNCBITaxonomyDatabase :: String -> IO (Either [String] NCBITaxDump) +readNCBITaxonomyDatabase folder = do + citations <- readNCBITaxCitations (folder ++ "citations.dmp") + let citationsError = extractParseError citations + taxdelNodes <- readNCBITaxDelNodes (folder ++ "delnodes.dmp") + let delNodesError = extractParseError taxdelNodes + divisons <- readNCBITaxDivisions (folder ++ "division.dmp") + let divisonsError = extractParseError divisons + genCodes <- readNCBITaxGenCodes (folder ++ "gencode.dmp") + let genCodesError = extractParseError genCodes + mergedNodes <- readNCBITaxMergedNodes (folder ++ "merged.dmp") + let mergedNodesError = extractParseError mergedNodes + names <- readNCBITaxNames (folder ++ "names.dmp") + let namesError = extractParseError names + taxnodes <- readNCBITaxNodes (folder ++ "nodes.dmp") + let nodesError = extractParseError taxnodes + let parseErrors = [citationsError, delNodesError, divisonsError, genCodesError, mergedNodesError, namesError, nodesError] + return (checkParsing parseErrors citations taxdelNodes divisons genCodes mergedNodes names taxnodes) + +genParserNCBITaxCitations :: GenParser Char st [TaxCitation] +genParserNCBITaxCitations = many1 genParserNCBITaxCitation + +genParserNCBITaxDelNodes :: GenParser Char st [TaxDelNode] +genParserNCBITaxDelNodes = many1 genParserNCBITaxDelNode + +genParserNCBITaxDivisons :: GenParser Char st [TaxDivision] +genParserNCBITaxDivisons = many1 genParserNCBITaxDivision + +genParserNCBITaxGenCodes :: GenParser Char st [TaxGenCode] +genParserNCBITaxGenCodes = many1 genParserNCBITaxGenCode + + +genParserNCBITaxMergedNodes :: GenParser Char st [TaxMergedNode] +genParserNCBITaxMergedNodes = many1 genParserNCBITaxMergedNode + + +genParserNCBITaxNames :: GenParser Char st [TaxName] +genParserNCBITaxNames = many1 genParserNCBITaxName + +genParserNCBITaxNodes :: GenParser Char st [TaxNode] +genParserNCBITaxNodes = many1 genParserNCBITaxNode + +genParserNCBISimpleTaxons :: GenParser Char st [SimpleTaxon] +genParserNCBISimpleTaxons = many1 genParserNCBISimpleTaxon + + +genParserNCBITaxCitation :: GenParser Char st TaxCitation +genParserNCBITaxCitation = do + _citId <- many1 digit + string "\t|\t" + _citKey <- optionMaybe (many1 (noneOf "\t")) + string "\t|\t" + _pubmedId <- optionMaybe (many1 digit) + string "\t|\t" + _medlineId <- optionMaybe (many1 digit) + tab + char '|' + _url <- genParserTaxURL + char '|' + tab + _text <- optionMaybe (many1 (noneOf "\t")) + string "\t|\t" + _taxIdList <- optionMaybe (many1 genParserTaxIdList) + string "\t|\n" + return $ TaxCitation (readInt _citId) _citKey (liftM readInt _pubmedId) (liftM readInt _medlineId) _url _text _taxIdList + +genParserNCBITaxDelNode :: GenParser Char st TaxDelNode +genParserNCBITaxDelNode = do + taxdelNode <- many1 digit + space + char '|' + char '\n' + return $ TaxDelNode (readInt taxdelNode) + +genParserNCBITaxDivision :: GenParser Char st TaxDivision +genParserNCBITaxDivision = do + _divisionId <- many1 digit + string "\t|\t" + _divisionCDE <- many1 upper + string "\t|\t" + _divisionName <- many1 (noneOf "\t") + string "\t|\t" + _comments <- optionMaybe (many1 (noneOf "\t")) + string "\t|\n" + return $ TaxDivision (readInt _divisionId) _divisionCDE _divisionName _comments + +genParserNCBITaxGenCode :: GenParser Char st TaxGenCode +genParserNCBITaxGenCode = do + _geneticCodeId <- many1 digit + string "\t|\t" + _abbreviation <- optionMaybe (many1 (noneOf "\t")) + string "\t|\t" + _genCodeName <- many1 (noneOf "\t") + string "\t|\t" + _cde <- many1 (noneOf "\t") + string "\t|\t" + _starts <- many1 (noneOf "\t") + string "\t|\n" + return $ TaxGenCode (readInt _geneticCodeId) _abbreviation _genCodeName _cde _starts + +genParserNCBITaxMergedNode :: GenParser Char st TaxMergedNode +genParserNCBITaxMergedNode = do + _oldTaxId <- many1 digit + string "\t|\t" + _newTaxId <- many1 digit + string "\t|\n" + return $ TaxMergedNode (readInt _oldTaxId) (readInt _newTaxId) + +genParserNCBITaxName :: GenParser Char st TaxName +genParserNCBITaxName = do + _taxId <- many1 digit + string "\t|\t" + _nameTxt <- many1 (noneOf "\t\n") + string "\t|\t" + _uniqueName <- optionMaybe (many1 (noneOf "\t\n")) + string "\t|\t" + _nameClass <- many1 (noneOf "\t\n") + tab + char '|' + newline + return $! TaxName (readInt _taxId) (B.pack _nameTxt) (maybe B.empty B.pack _uniqueName) (B.pack _nameClass) + +genParserNCBISimpleTaxon :: GenParser Char st SimpleTaxon +genParserNCBISimpleTaxon = do + _simpleTaxId <- many1 digit + string "\t|\t" + _simpleParentTaxId <- many1 digit + string "\t|\t" + _simpleRank <- many1 (noneOf "\t") + many1 (noneOf "\n") + char '\n' + return $! SimpleTaxon (readInt _simpleTaxId) B.empty (readInt _simpleParentTaxId) (readRank _simpleRank) + +genParserNCBITaxNode :: GenParser Char st TaxNode +genParserNCBITaxNode = do + _taxId <- many1 digit + string "\t|\t" + _parentTaxId <- many1 digit + string "\t|\t" + _rank <- many1 (noneOf "\t") + string "\t|\t" + _emblCode <- optionMaybe (many1 (noneOf "\t")) + string "\t|\t" + _divisionId <- many1 digit + string "\t|\t" + _inheritedDivFlag <- many1 digit + string "\t|\t" + _geneticCodeId <- many1 digit + string "\t|\t" + _inheritedGCFlag <- many1 digit + string "\t|\t" + _mitochondrialGeneticCodeId <- many1 digit + string "\t|\t" + _inheritedMGCFlag <- many1 digit + string "\t|\t" + _genBankHiddenFlag <- many1 digit + string "\t|\t" + _hiddenSubtreeRootFlag <- many1 digit + string "\t|\t" + _comments <- optionMaybe (many1 (noneOf "\t")) + tab + char '|' + char '\n' + return $ TaxNode (readInt _taxId) (readInt _parentTaxId) (readRank _rank) _emblCode _divisionId (readBool _inheritedDivFlag) _geneticCodeId (readBool _inheritedGCFlag) _mitochondrialGeneticCodeId (readBool _inheritedMGCFlag) (readBool _genBankHiddenFlag) (readBool _hiddenSubtreeRootFlag) _comments + +--------------------------------------- +-- Processing functions + +-- | Extract a subtree correpsonding to input node paths to root. Only nodes in level number distance to root are included. Used in Ids2TreeCompare tool. +compareSubTrees :: [Gr SimpleTaxon Double] -> (Int,Gr CompareTaxon Double) +compareSubTrees graphs = (length graphs,resultGraph) + where treesLabNodes = map labNodes graphs + treesLabEdges = map labEdges graphs + mergedNodes = nub (concat treesLabNodes) + mergedEdges = nub (concat treesLabEdges) + --annotate node in which of the compared trees they are present + comparedNodes = annotateTaxonsDifference treesLabNodes mergedNodes + resultGraph = mkGraph comparedNodes mergedEdges :: Gr CompareTaxon Double + +annotateTaxonsDifference :: [[LNode SimpleTaxon]] -> [LNode SimpleTaxon] -> [LNode CompareTaxon] +annotateTaxonsDifference treesNodes mergedtreeNodes = comparedNodes + where comparedNodes = map (annotateTaxonDifference indexedTreesNodes) mergedtreeNodes + indexedTreesNodes = zip [0..(length treesNodes)] treesNodes + + +annotateTaxonDifference :: [(Int,[LNode SimpleTaxon])] -> LNode SimpleTaxon -> LNode CompareTaxon +annotateTaxonDifference indexedTreesNodes mergedtreeNode = comparedNode + where comparedNode = (simpleTaxId (snd mergedtreeNode),CompareTaxon (simpleScientificName (snd mergedtreeNode)) (simpleRank (snd mergedtreeNode)) currentInTree) + currentInTree = concatMap (\(i,treeNodes) -> [i | mergedtreeNode `elem` treeNodes]) indexedTreesNodes + +-- | Extract a subtree corresponding to input node paths to root. Only nodes in level number distance to root are included. Used in Ids2Tree tool. +extractTaxonomySubTreebyLevel :: [Node] -> Gr SimpleTaxon Double -> Maybe Int -> Gr SimpleTaxon Double +extractTaxonomySubTreebyLevel inputNodes graph levelNumber = taxonomySubTree + where paths = nub (concatMap (getPath (1 :: Node) graph) inputNodes) + contexts = map (context graph) paths + lnodes = map labNode' contexts + ledges = nub (concatMap (out graph . fst) lnodes) + unfilteredTaxonomySubTree = mkGraph lnodes ledges :: Gr SimpleTaxon Double + filteredLNodes = filterNodesByLevel levelNumber lnodes unfilteredTaxonomySubTree + filteredledges = nub (concatMap (out graph . fst) filteredLNodes) + taxonomySubTree = mkGraph filteredLNodes filteredledges :: Gr SimpleTaxon Double + +-- | Extract a subtree corresponding to input node paths to root. If a Rank is provided, all node that are less or equal are omitted +extractTaxonomySubTreebyRank :: [Node] -> Gr SimpleTaxon Double -> Maybe Rank -> Gr SimpleTaxon Double +extractTaxonomySubTreebyRank inputNodes graph highestRank = taxonomySubTree + where paths = nub (concatMap (getPath (1 :: Node) graph) inputNodes) + contexts = map (context graph) paths + lnodes = map labNode' contexts + filteredLNodes = filterNodesByRank highestRank lnodes + filteredledges = nub (concatMap (out graph . fst) filteredLNodes) + taxonomySubTree = mkGraph filteredLNodes filteredledges :: Gr SimpleTaxon Double + +getPath :: Node -> Gr SimpleTaxon Double -> Node -> Path +getPath root graph node = sp node root graph + +-- | Extract parent node with specified Rank +getParentbyRank :: Node -> Gr SimpleTaxon Double -> Maybe Rank -> Maybe (Node, SimpleTaxon) +getParentbyRank inputNode graph requestedRank = filteredLNode + where path = sp (inputNode :: Node) (1 :: Node) graph + nodeContext = map (context graph) path + lnode = map labNode' nodeContext + filteredLNode = findNodeByRank requestedRank lnode + +-- | Filter nodes by distance from root +filterNodesByLevel :: Maybe Int -> [(Node, SimpleTaxon)] -> Gr SimpleTaxon Double -> [(Node, SimpleTaxon)] +filterNodesByLevel levelNumber inputNodes graph + | isJust levelNumber = filteredNodes + | otherwise = inputNodes + --distances of all nodes to root + where nodedistances = level (1::Node) (undir graph) + sortedNodeDistances = sortBy sortByNodeID nodedistances + sortedInputNodes = sortBy sortByNodeID inputNodes + zippedNodeDistancesInputNodes = zip sortedNodeDistances sortedInputNodes + zippedFilteredNodes = filter (\((_,distance),(_,_)) -> distance <= fromJust levelNumber) zippedNodeDistancesInputNodes + filteredNodes = map snd zippedFilteredNodes + +sortByNodeID :: (Node,a) -> (Node,a) -> Ordering +sortByNodeID (n1, _) (n2, _) + | n1 < n2 = GT + | n1 > n2 = LT + | n1 == n2 = EQ + | otherwise = EQ + +-- | Find only taxons of a specific rank in a list of input taxons +findNodeByRank :: Maybe Rank -> [(t, SimpleTaxon)] -> Maybe (t, SimpleTaxon) +findNodeByRank requestedRank inputNodes + | isJust requestedRank = filteredNodes + | otherwise = Nothing + where filteredNodes = find (\(_,t) -> simpleRank t == fromJust requestedRank) inputNodes + +-- | Filter a list of input taxons for a minimal provided rank +filterNodesByRank :: Maybe Rank -> [(t, SimpleTaxon)] -> [(t, SimpleTaxon)] +filterNodesByRank highestRank inputNodes + | isJust highestRank = filteredNodes + | otherwise = inputNodes + where filteredNodes = filter (\(_,t) -> simpleRank t >= fromJust highestRank) inputNodes ++ noRankNodes + noRankNodes = filter (\(_,t) -> simpleRank t == Norank) inputNodes + +-- | Returns path between 2 maybe nodes. Used in TreeDistance tool. +safeNodePath :: Maybe Node -> Gr SimpleTaxon Double -> Maybe Node -> Either String [Node] +safeNodePath nodeid1 graphOutput nodeid2 + | isJust nodeid1 && isJust nodeid2 = Right (sp (fromJust nodeid1) (fromJust nodeid2) (undir graphOutput)) + | otherwise = Left "Both taxonomy ids must be provided for distance computation" + +--------------------------------------- +-- Visualisation functions + +-- | Draw graph in dot format. Used in Ids2Tree tool. +drawTaxonomy :: Gr SimpleTaxon Double -> String +drawTaxonomy inputGraph = do + let params = GV.nonClusteredParams {GV.isDirected = True + , GV.globalAttributes = [GV.GraphAttrs [GVA.Size (GVA.GSize (20 :: Double) (Just (20 :: Double)) False)]] + , GV.isDotCluster = const True + , GV.fmtNode = \ (_,l) -> [GV.textLabel (TL.pack (show (simpleRank l) ++ "\n" ++ B.unpack (simpleScientificName l)))] + , GV.fmtEdge = const [] + } + let dotFormat = GV.graphToDot params inputGraph + let dottext = GVP.renderDot $ GVP.toDot dotFormat + TL.unpack dottext + +-- | Draw tree comparison graph in dot format. Used in Ids2TreeCompare tool. +drawTreeComparison :: (Int,Gr CompareTaxon Double) -> String +drawTreeComparison (treeNumber,inputGraph) = do + let cList = makeColorList treeNumber + let params = GV.nonClusteredParams {GV.isDirected = True + , GV.globalAttributes = [] + , GV.isDotCluster = const True + , GV.fmtNode = \ (_,l) -> [GV.textLabel (TL.pack (show (compareRank l) ++ "\n" ++ B.unpack (compareScientificName l))), GV.style GV.wedged, GVA.Color (selectColors (inTree l) cList)] + , GV.fmtEdge = const [] + } + let dotFormat = GV.graphToDot params (grev inputGraph) + let dottext = GVP.renderDot $ GVP.toDot dotFormat + TL.unpack dottext + +-- | Colors from color list are selected according to in which of the compared trees the node is contained. +selectColors :: [Int] -> [GVA.Color] -> GVAC.ColorList +selectColors inTrees currentColorList = GVAC.toColorList (map (\i -> currentColorList !! i) inTrees) + +-- | A color list is sampled from the spectrum according to how many trees are compared. +makeColorList :: Int -> [GVA.Color] +makeColorList treeNumber = cList + where cList = map (\i -> GVAC.HSV ((fromIntegral i/fromIntegral neededColors) * 0.708) 0.5 1.0) [0..neededColors] + neededColors = treeNumber - 1 + +-- | Write tree representation either as dot or json to provided file path +writeTree :: String -> String -> Gr SimpleTaxon Double -> IO () +writeTree requestedFormat outputDirectoryPath inputGraph = do + case requestedFormat of + "dot" -> writeDotTree outputDirectoryPath inputGraph + "json"-> writeJsonTree outputDirectoryPath inputGraph + _ -> writeDotTree outputDirectoryPath inputGraph + +-- | Write tree representation as dot to provided file path. +-- Graphviz tools like dot can be applied to the written .dot file to generate e.g. svg-format images. +writeDotTree :: String -> Gr SimpleTaxon Double -> IO () +writeDotTree outputDirectoryPath inputGraph = do + let diagram = drawTaxonomy (grev inputGraph) + writeFile (outputDirectoryPath ++ "taxonomy.dot") diagram + +-- | Write tree representation as json to provided file path. +-- You can visualize the result for example with 3Djs. +writeJsonTree :: String -> Gr SimpleTaxon Double -> IO () +writeJsonTree outputDirectoryPath inputGraph = do + let jsonOutput = AE.encode (grev inputGraph) + L.writeFile (outputDirectoryPath ++ "taxonomy.json") jsonOutput + +--------------------------------------- +-- Auxiliary functions +readInt :: String -> Int +readInt = read + +readBool :: String -> Bool +readBool "0" = False +readBool "1" = True +readBool _ = False + +readRank :: String -> Rank +readRank a = read a :: Rank + +genParserTaxIdList :: GenParser Char st Int +genParserTaxIdList = do + optional (char ' ') + _taxId <- many1 digit + optional (char ' ') + return (readInt _taxId) + +genParserTaxURL :: GenParser Char st (Maybe String) +genParserTaxURL = do + tab + url1 <- optionMaybe (many1 (noneOf "\t")) + tab + url2 <- optionMaybe (many1 (noneOf "|")) + return (concatenateURLParts url1 url2) + +concatenateURLParts :: Maybe String -> Maybe String -> Maybe String +concatenateURLParts url1 url2 + | isJust url1 && isJust url2 = maybeStringConcat url1 url2 + | isJust url1 && isNothing url2 = url1 + | otherwise = Nothing + +maybeStringConcat :: Maybe String -> Maybe String -> Maybe String +maybeStringConcat = liftM2 (++) + +readEncodedFile :: TextEncoding -> FilePath -> IO String +readEncodedFile encoding name = do + handle <- openFile name ReadMode + hSetEncoding handle encoding + hGetContents handle + +parseFromFileEncISO88591 :: Parser a -> String -> IO (Either ParseError a) +parseFromFileEncISO88591 parser fname = do + input <- readEncodedFile latin1 fname + return (runP parser () fname input) + +-- | check a list of parsing results for presence of Left aka Parse error +checkParsing :: [String] -> Either ParseError [TaxCitation] -> Either ParseError [TaxDelNode] -> Either ParseError [TaxDivision] -> Either ParseError [TaxGenCode] -> Either ParseError [TaxMergedNode] -> Either ParseError [TaxName] -> Either ParseError [TaxNode]-> Either [String] NCBITaxDump +checkParsing parseErrors citations taxdelNodes divisons genCodes mergedNodes names taxnodes + | join parseErrors == "" = Right (NCBITaxDump (E.fromRight citations) (E.fromRight taxdelNodes) (E.fromRight divisons) (E.fromRight genCodes) (E.fromRight mergedNodes) (E.fromRight names) (E.fromRight taxnodes)) + | otherwise = Left parseErrors + +extractParseError :: Either ParseError a -> String +extractParseError _parse + | E.isLeft _parse = show (E.fromLeft _parse) + | otherwise = "" diff --git a/src/Bio/TaxonomyData.hs b/src/Bio/TaxonomyData.hs new file mode 100644 --- /dev/null +++ b/src/Bio/TaxonomyData.hs @@ -0,0 +1,289 @@ +-- | This module contains data structures for +-- taxonomy data + +{-# LANGUAGE FlexibleInstances #-} + +module Bio.TaxonomyData where +import Prelude +import qualified Data.ByteString as B +import qualified Data.Aeson as A +import qualified Data.Vector as V +import Data.Graph.Inductive +import qualified Data.Text as T +import qualified Data.Text.Encoding + +-- | SimpleTaxon only contains the most relevant fields of a taxonomy entry. +-- For all annotaded fields use the Taxon datatype and its associated functions +data SimpleTaxon = SimpleTaxon + { + -- node id in GenBank + simpleTaxId :: Int, + simpleScientificName :: B.ByteString, + -- parent node id in GenBank taxonomy database + simpleParentTaxId :: Int, + -- rank of this node (superkingdom, kingdom, ...) + simpleRank :: Rank + } + deriving (Show, Read, Eq) + +-- | Datastructure for tree comparisons +data CompareTaxon = CompareTaxon + { + compareScientificName :: B.ByteString, + compareRank :: Rank, + -- number indicating in which trees, + inTree :: [Int] + } + deriving (Show, Read, Eq) + +-- | Data structure for Entrez taxonomy fetch result +data Taxon = Taxon + { taxonTaxId :: Int + , taxonScientificName :: String + , taxonParentTaxId :: Int + , taxonRank :: Rank + , division :: String + , geneticCode :: TaxGenCode + , mitoGeneticCode :: TaxGenCode + , lineage :: String + , lineageEx :: [LineageTaxon] + , createDate :: String + , updateDate :: String + , pubDate :: String + } deriving (Show, Eq) + + +data TaxonName = TaxonName + { classCDE :: String + , dispName :: String + } deriving (Show, Eq) + +-- | Lineage Taxons denote all parent Taxonomy nodes of a node retrieved by Entrez fetch +data LineageTaxon = LineageTaxon + { lineageTaxId :: Int + , lineageScienticName :: String + , lineageRank :: Rank} + deriving (Show, Eq) + +-- | NCBI Taxonomy database dump hierachichal data structure +-- as defined in ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_readme.txt +data NCBITaxDump = NCBITaxDump + { + taxCitations :: [TaxCitation], + taxDelNodes :: [TaxDelNode], + taxDivisions :: [TaxDivision], + taxGenCodes :: [TaxGenCode], + taxMergedNodes :: [TaxMergedNode], + taxNames :: [TaxName], + taxNodes :: [TaxNode] + } + deriving (Show, Read, Eq) + +-- | Datastructure for entries of Taxonomy database dump citations file +data TaxCitation = TaxCitation + { + -- the unique id of citation + citId :: Int, + -- citation key + citKey :: Maybe String, + -- unique id in PubMed database (0 if not in PubMed) + pubmedId :: Maybe Int, + -- unique id in MedLine database (0 if not in MedLine) + medlineId :: Maybe Int, + -- URL associated with citation + url :: Maybe String, + -- any text (usually article name and authors) + -- The following characters are escaped in this text by a backslash: + -- newline (appear as "\n"), + -- tab character ("\t"), + -- double quotes ('\"'), + -- backslash character ("\\"). + text :: Maybe String, + -- list of node ids separated by a single space + taxIdList :: Maybe [Int] + } + deriving (Show, Read, Eq) + +-- | Datastructure for entries of Taxonomy database dump deleted nodes file +data TaxDelNode = TaxDelNode + { + -- deleted node id + delTaxId :: Int + } + deriving (Show, Read, Eq) + +-- | Datastructure for entries of Taxonomy database dump division file +data TaxDivision = TaxDivision + { + -- taxonomy database division id + divisionId :: Int, + -- GenBank division code (three characters) + divisionCDE :: String, + -- e.g. BCT, PLN, VRT, MAM, PRI... + divisonName :: String, + divisionComments :: Maybe String + } + deriving (Show, Read, Eq) + +-- | Datastructure for entries of Taxonomy database dump gencode file +data TaxGenCode = TaxGenCode + { + -- GenBank genetic code id + geneticCodeId :: Int, + -- genetic code name abbreviation + abbreviation :: Maybe String, + -- genetic code name + geneCodeName :: String, + -- translation table for this genetic code + cde :: String, + -- start codons for this genetic code + starts :: String + } + deriving (Show, Read, Eq) + +-- | Datastructure for entries of Taxonomy database dump mergednodes file +data TaxMergedNode = TaxMergedNode + { + -- id of nodes which has been merged + oldTaxId :: Int, + -- id of nodes which is result of merging + newTaxId :: Int + } + deriving (Show, Read, Eq) + +-- | Datastructure for entries of Taxonomy database dump names file +data TaxName = TaxName + { + -- the id of node associated with this name + nameTaxId :: Int, + -- name itself + nameTxt :: B.ByteString, + -- the unique variant of this name if name not unique + uniqueName :: B.ByteString, + -- (synonym, common name, ...) + nameClass :: B.ByteString + } + deriving (Show, Read, Eq) + +-- | Taxonomic ranks: NCBI uses the uncommon Speciessubgroup +data Rank = Norank | Form | Variety | Infraspecies | Subspecies | Speciessubgroup | Species | Speciesgroup | Superspecies | Series | Section | Subgenus | Genus | Subtribe | Tribe | Supertribe | Subfamily | Family | Superfamily | Parvorder | Infraorder | Suborder | Order | Superorder | Magnorder | Cohort | Legion | Parvclass | Infraclass | Subclass | Class | Superclass | Microphylum | Infraphylum | Subphylum | Phylum | Superphylum | Infrakingdom | Subkingdom | Kingdom | Superkingdom | Domain deriving (Eq, Ord, Show, Bounded, Enum) + +readsRank :: String -> [(Rank, String)] +instance Read Rank where + readsPrec _ = readsRank + +readsRank input -- = [(Domain x)| x <- reads input ] + | input == "domain" = [(Domain,"")] + | input == "superkingdom" = [(Superkingdom,"")] + | input == "kingdom" = [(Kingdom,"")] + | input == "subkingdom" = [(Subkingdom,"")] + | input == "infrakingdom" = [(Infrakingdom,"")] + | input == "superphylum" = [(Superphylum,"")] + | input == "phylum" = [(Phylum,"")] + | input == "subphylum" = [(Subphylum,"")] + | input == "infraphylum" = [(Infraphylum,"")] + | input == "microphylum" = [(Microphylum,"")] + | input == "superclass" = [(Superclass,"")] + | input == "class" = [(Class,"")] + | input == "subclass" = [(Subclass,"")] + | input == "infraclass" = [(Infraclass,"")] + | input == "parvclass " = [(Parvclass ,"")] + | input == "legion" = [(Legion,"")] + | input == "cohort" = [(Cohort,"")] + | input == "magnorder " = [(Magnorder ,"")] + | input == "superorder" = [(Superorder,"")] + | input == "order" = [(Order,"")] + | input == "suborder" = [(Suborder,"")] + | input == "infraorder" = [(Infraorder,"")] + | input == "parvorder" = [(Parvorder,"")] + | input == "superfamily" = [(Superfamily,"")] + | input == "family" = [(Family,"")] + | input == "subfamily" = [(Subfamily,"")] + | input == "supertribe" = [(Supertribe,"")] + | input == "tribe" = [(Tribe,"")] + | input == "subtribe" = [(Subtribe,"")] + | input == "genus" = [(Genus,"")] + | input == "subgenus" = [(Subgenus,"")] + | input == "section" = [(Section,"")] + | input == "series" = [(Series,"")] + | input == "superspecies" = [(Superspecies,"")] + | input == "species group" = [(Speciesgroup,"")] + | input == "species" = [(Species,"")] + | input == "species subgroup" = [(Speciessubgroup,"")] + | input == "subspecies" = [(Subspecies,"")] + | input == "infraspecies" = [(Infraspecies,"")] + | input == "varietas" = [(Variety,"")] + | input == "forma" = [(Form,"")] + | input == "no rank" = [(Norank,"")] + | otherwise = [(Norank,"")] + +-- | Datastructure for entries of Taxonomy database dump nodes file +data TaxNode = TaxNode + { + -- node id in GenBank + taxId :: Int, + -- parent node id in GenBank taxonomy database + parentTaxId :: Int, + -- rank of this node (superkingdom, kingdom, ...) + rank :: Rank, + -- locus-name prefix; not unique + emblCode :: Maybe String, + -- see division.dmp file + nodeDivisionId :: String, + -- 1 if node inherits division from parent + inheritedDivFlag :: Bool, + -- see gencode.dmp file + nodeGeneticCodeId :: String, + -- 1 if node inherits genetic code from parent + inheritedGCFlag :: Bool, + -- see gencode.dmp file + mitochondrialGeneticCodeId :: String, + -- 1 if node inherits mitochondrial gencode from parent + inheritedMGCFlag :: Bool, + -- 1 if name is suppressed in GenBank entry lineage + genBankHiddenFlag :: Bool, + -- 1 if this subtree has no sequence data yet + hiddenSubtreeRootFlag :: Bool, + -- free-text comments and citations + nodeComments :: Maybe String + } + deriving (Show, Read, Eq) + +-- | Simple Gene2Accession table +data SimpleGene2Accession = SimpleGene2Accession + { simpleTaxIdEntry :: Int, + simpleGenomicNucleotideAccessionVersion :: String + } deriving (Show, Eq, Read) + +-- | Datastructure for Gene2Accession table +data Gene2Accession = Gene2Accession + { taxIdEntry :: Int, + geneID :: Int, + status :: String, + rnaNucleotideAccessionVersion :: String, + rnaNucleotideGi :: String, + proteinAccessionVersion :: String, + proteinGi :: String, + genomicNucleotideAccessionVersion :: String, + genomicNucleotideGi :: String, + startPositionOnTheGenomicAccession :: String, + endPositionOnTheGenomicAccession :: String, + orientation :: String, + assembly :: String, + maturePeptideAccessionVersion :: String, + maturePeptideGi :: String + } deriving (Show, Eq, Read) + +instance A.ToJSON (Gr SimpleTaxon Double) where + toJSON inputGraph = simpleTaxonJSONValue inputGraph 1 + +simpleTaxonJSONValue :: Gr SimpleTaxon Double -> Node -> A.Value +simpleTaxonJSONValue inputGraph node = jsonValue + where jsonValue = A.object [currentScientificName,T.pack "children" A..= children] + childNodes = suc inputGraph node + currentLabel = lab inputGraph node + currentScientificName = T.pack "name" A..= maybe (T.pack "notFound") (Data.Text.Encoding.decodeUtf8 . simpleScientificName) currentLabel + children = A.Array (V.fromList (map (simpleTaxonJSONValue inputGraph) childNodes)) + --jsonValue = A.object [currentScientificName,currentId,currentRank,(T.pack "children") A..= children] + --currentId = (T.pack "id") A..= (maybe (T.pack "notFound") (\a -> T.pack (show (simpleTaxId a))) currentLabel) + --currentRank = (T.pack "rank") A..= (maybe (T.pack "notFound") (\a -> T.pack (show (simpleRank a))) currentLabel)