Taxonomy (empty) → 1.0.1
raw patch · 5 files changed
+1607/−0 lines, 5 filesdep +aesondep +basedep +bytestringsetup-changed
Dependencies added: aeson, base, bytestring, either-unwrap, fgl, graphviz, parsec, text, vector
Files
- LICENSE +675/−0
- Setup.hs +2/−0
- Taxonomy.cabal +58/−0
- src/Bio/Taxonomy.hs +583/−0
- src/Bio/TaxonomyData.hs +289/−0
+ LICENSE view
@@ -0,0 +1,675 @@+ GNU GENERAL PUBLIC LICENSE+ Version 3, 29 June 2007++ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>+ Everyone is permitted to copy and distribute verbatim copies+ of this license document, but changing it is not allowed.++ Preamble++ The GNU General Public License is a free, copyleft license for+software and other kinds of works.++ The licenses for most software and other practical works are designed+to take away your freedom to share and change the works. By contrast,+the GNU General Public License is intended to guarantee your freedom to+share and change all versions of a program--to make sure it remains free+software for all its users. We, the Free Software Foundation, use the+GNU General Public License for most of our software; it applies also to+any other work released this way by its authors. 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
+ Taxonomy.cabal view
@@ -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 <http://www.ncbi.nlm.nih.gov/taxonomy Entrez> REST interface via <https://github.com/eggzilla/EntrezHTTP EntrezHTTP>,+ as well as from the files of the Taxonomy database <ftp://ftp.ncbi.nih.gov/pub/taxonomy/ dump>.+ .+ 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 (<http://graphviz.org/ graphviz>)+ .+ <<http://www.tbi.univie.ac.at/~egg/taxonomy.svg dot>> + .+ or via json-format (<http://d3js.org/d3js>).+ .+ The <https://hackage.haskell.org/package/TaxonomyTools TaxonomyTools> 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+
+ src/Bio/Taxonomy.hs view
@@ -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 = ""
+ src/Bio/TaxonomyData.hs view
@@ -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)