diff --git a/Biobase/Ensembl/HTTP.hs b/Biobase/Ensembl/HTTP.hs new file mode 100644 --- /dev/null +++ b/Biobase/Ensembl/HTTP.hs @@ -0,0 +1,74 @@ +{-# LANGUAGE OverloadedStrings #-} +-- | Interface for Ensembl + +module Biobase.Ensembl.HTTP ( + startXRefSession, + requestGOTermsWithGeneIds, + requestUniProtWithGeneIds, + EnsemblEntry(..) + ) where + +import Network.HTTP.Conduit +import qualified Data.ByteString.Lazy.Char8 as L8 +import Network.Socket +import Data.Aeson +import Data.Either.Unwrap +import Biobase.Ensembl.REST.Types +import Control.Concurrent +import Data.Maybe +import Data.List +import qualified Data.Text as T + +requestGOTermsWithGeneIds :: [T.Text] -> IO [(T.Text,[T.Text])] +requestGOTermsWithGeneIds geneIds = do + let queryParameters = T.pack "?external_db=GO;all_levels=1;content-type=application/json" + mapM (requestGOTermsWithGeneId queryParameters) geneIds + +requestGOTermsWithGeneId :: T.Text -> T.Text -> IO (T.Text,[T.Text]) +requestGOTermsWithGeneId queryParameters geneId = do + --let protid= "AAC73113" + responseJson <- startXRefSession queryParameters geneId + --3/s + threadDelay 330000 + if isRight responseJson + then return (geneId,(extractGOTerms (fromRight responseJson))) + else return (geneId,[]) + +extractGOTerms :: [EnsemblEntry] -> [T.Text] +extractGOTerms entries = goTerms + where goEntries = filter (\a -> T.pack "GO" == fromMaybe "" (dbname a)) entries + goTerms = map (fromJust . display_id) goEntries + +requestUniProtWithGeneIds :: [T.Text] -> IO [(T.Text,T.Text)] +requestUniProtWithGeneIds geneIds = do + let queryParameters = T.pack "?external_db=Uniprot/SWISSPROT;all_levels=1;content-type=application/json" + mapM (requestUniProtWithGeneId queryParameters) geneIds + +requestUniProtWithGeneId :: T.Text -> T.Text -> IO (T.Text,T.Text) +requestUniProtWithGeneId queryParameters geneId = do + --let protid= "AAC73113" + responseJson <- startXRefSession queryParameters geneId + -- 3/s + threadDelay 330000 + if isRight responseJson + then return (geneId,(extractUniProtId (fromRight responseJson))) + else return (geneId,T.empty) + +extractUniProtId :: [EnsemblEntry] -> T.Text +extractUniProtId entries = uniprotName + where uniprotEntry = find (\a -> T.pack "Uniprot/SWISSPROT" == fromMaybe "" (dbname a)) entries + uniprotName = if isJust uniprotEntry then fromMaybe T.empty (display_id (fromJust uniprotEntry)) else T.empty + +startXRefSession :: T.Text -> T.Text -> IO (Either String [EnsemblEntry]) +startXRefSession queryParameters xrefId = do + response <- withSocketsDo + $ sendXRefQuery xrefId queryParameters + let decodedJson = eitherDecode response :: Either String [EnsemblEntry] + return decodedJson + +--"[{\"display_id\":\"00300+2.7.2.4+1.1.1.3\",\"primary_id\":\"00300+2.7.2.4+1.1.1.3\",\"version\":\"0\",\"description\":\"\",\"dbname\":\"KEGG_Enzyme\",\"synonyms\":[],\"info_text\":\"\",\"info_type\":\"NONE\",\"db_display_name\":\"KEGG Pathway and Enzyme\"}]"" + +-- | Send query and return response +-- http://rest.ensemblgenomes.org/xrefs/id/AAC73113?content-type=application/json +sendXRefQuery :: T.Text -> T.Text -> IO L8.ByteString +sendXRefQuery xrefId queryParameters = simpleHttp ("http://rest.ensemblgenomes.org/xrefs/id/" ++ T.unpack xrefId ++ T.unpack queryParameters) diff --git a/Biobase/Entrez/HTTP.hs b/Biobase/Entrez/HTTP.hs new file mode 100644 --- /dev/null +++ b/Biobase/Entrez/HTTP.hs @@ -0,0 +1,417 @@ +{-# LANGUAGE OverloadedStrings #-} +{-# LANGUAGE Arrows #-} + +-- | Interface for the NCBI Entrez REST webservice. +-- +-- The entrezHTTP function provides a interface to the NCBI Entrez REST service. +-- +-- A series of different eutilites and databases are provided by the REST interface. +-- Response depends on the combination of eutil and database, as well requested returntype. +-- Specific combinations have wrapper functions with corresponding parsing functions included (see Usage example). +-- +-- If you use this libary in a tool, please read carefully and register your tool at eutilities@ncbi.nlm.nih.gov. You can append your registration info generated +-- with the included buildRegistration function to your query. +-- +-- == Usage example: +-- +-- Retrieve a nucleotide sequence for Escherichia coli +-- +-- > nucleotideFasta <- fetchNucleotideString "NC_000913.3" 50 1000 "+" Nothing + +module Biobase.Entrez.HTTP (-- * Datatypes + module Biobase.Entrez.HTTPData, + -- * Retrieval function + entrezHTTP, + retrieveGeneSymbolFasta, + fetchNucleotideString, + retrieveElementsEntrez, + portionListElements, + -- * Parsing functions + readEntrezTaxonSet, + readEntrezSimpleTaxons, + readEntrezParentIds, + readEntrezSummaries, + readEntrezSearch, + -- * auxiliary functions + buildRegistration, + maybeBuildRegistration, + setStrand, + convertCoordinatesToStrand + ) where + +import Network.HTTP.Conduit +import qualified Data.ByteString.Lazy.Char8 as L8 +import Text.XML.HXT.Core +import Network.Socket +import Data.Maybe +import Biobase.Entrez.HTTPData +import Bio.TaxonomyData +import Network.HTTP.Base +import qualified Data.Text.Lazy as TL + +-- | Send query and parse return XML +startSession :: String -> String -> String -> IO String +startSession program' database' query' = do + requestXml <- withSocketsDo + $ sendQuery program' database' query' + let requestXMLString = L8.unpack requestXml + return requestXMLString + +-- | Send query and return response XML +sendQuery :: String -> String -> String -> IO L8.ByteString +sendQuery program' database' query' = simpleHttp ("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"++ program' ++ ".fcgi?" ++ "db=" ++ database' ++ "&" ++ query') + +-- | Function for querying the NCBI entrez REST interface. Input EntrezHTTPQuery datatype is used to select database, program of interest and contains the query string. +-- Please note that query strings containing whitespace or special characters need to be urlencoded. The response format and content depends on the query type, the output +-- therefore provided as String. +entrezHTTP :: EntrezHTTPQuery -> IO String +entrezHTTP (EntrezHTTPQuery program' database' query') = do + let defaultProgram = "summary" + let defaultDatabase = "nucleotide" + let selectedProgram = fromMaybe defaultProgram program' + let selectedDatabase = fromMaybe defaultDatabase database' + startSession selectedProgram selectedDatabase query' + +-- | Wrapper function for eutils that accept a list of querys (e.g. a list of gene ids) that ensures that only chunks of 20 queries are sent per request. Sending to long queries otherwise results in a serverside exception. +retrieveElementsEntrez :: [a] -> ([a] -> IO b) -> IO [b] +retrieveElementsEntrez listElements retrievalfunction = do + let splits = portionListElements listElements 20 + mapM retrievalfunction splits + +-- Auxiliary function for retrieveElementsEntrez +portionListElements :: [a] -> Int -> [[a]] +portionListElements listElements elementsPerSplit + | not (null listElements) = filter (not . null) result + | otherwise = [] + where (heads,xs) = splitAt elementsPerSplit listElements + result = heads:portionListElements xs elementsPerSplit + +--------------------------------------- +-- Parsing functions + +-- | Read entrez fetch for taxonomy database into a simplyfied datatype +-- Result of e.g: http://eutils.ncbi.nlm.nih. +readEntrezTaxonSet :: String -> [Taxon] +readEntrezTaxonSet = runLA (xreadDoc >>> parseEntrezTaxonSet) + +parseEntrezTaxonSet :: ArrowXml a => a XmlTree Taxon +parseEntrezTaxonSet = atTag "TaxaSet" >>> getChildren >>> + proc entrezTaxons -> do + _taxons <- parseEntrezTaxon -< entrezTaxons + returnA -< _taxons + +parseEntrezTaxon :: ArrowXml a => a XmlTree Taxon +parseEntrezTaxon = (isElem >>> hasName "Taxon") >>> + proc entrezTaxon -> do + _taxonomyId <- getChildren >>> (isElem >>> hasName "TaxId") >>> getChildren >>> getText -< entrezTaxon + _scientificName <- getChildren >>> (isElem >>> hasName "ScientificName") >>> getChildren >>> getText -< entrezTaxon + _parentTaxonomyId <- getChildren >>> (isElem >>> hasName "ParentTaxId") >>> getChildren >>> getText -< entrezTaxon + _rank <- getChildren >>> (isElem >>> hasName "Rank") >>> getChildren >>> getText -< entrezTaxon + _divison <- getChildren >>> (isElem >>> hasName "Division") >>> getChildren >>> getText -< entrezTaxon + _geneticCode <- parseTaxonGeneticCode -< entrezTaxon + _mitoGeneticCode <- parseTaxonMitoGeneticCode -< entrezTaxon + _lineage <- getChildren >>> atTag "Lineage" >>> getChildren >>> getText -< entrezTaxon + _lineageEx <- parseTaxonLineageEx -< entrezTaxon + _createDate <- getChildren >>> (isElem >>> hasName "CreateDate") >>> getChildren >>> getText -< entrezTaxon + _updateDate <- getChildren >>> (isElem >>> hasName "UpdateDate") >>> getChildren >>> getText -< entrezTaxon + _pubDate <- getChildren >>> (isElem >>> hasName "PubDate") >>> getChildren >>> getText -< entrezTaxon + returnA -< Taxon { + taxonTaxId = read _taxonomyId :: Int, + taxonScientificName = _scientificName, + taxonParentTaxId = read _parentTaxonomyId :: Int, + taxonRank = read _rank :: Rank, + division = _divison, + geneticCode = _geneticCode, + mitoGeneticCode = _mitoGeneticCode, + lineage = _lineage, + lineageEx = _lineageEx, + createDate = _createDate, + updateDate = _updateDate, + pubDate = _pubDate + } + +parseTaxonGeneticCode :: ArrowXml a => a XmlTree TaxGenCode +parseTaxonGeneticCode = getChildren >>> atTag "GeneticCode" >>> + proc geneticcode -> do + _gcId <- atTag "GCId" >>> getChildren >>> getText -< geneticcode + _gcName <- atTag "GCName" >>> getChildren >>> getText -< geneticcode + returnA -< TaxGenCode { + geneticCodeId = read _gcId :: Int, + abbreviation = Nothing, + geneCodeName = _gcName, + cde = [], + starts = [] + } + +parseTaxonMitoGeneticCode :: ArrowXml a => a XmlTree TaxGenCode +parseTaxonMitoGeneticCode = getChildren >>> atTag "MitoGeneticCode" >>> + proc mitogeneticcode -> do + _mgcId <- atTag "MGCId" >>> getChildren >>> getText -< mitogeneticcode + _mgcName <- atTag "MGCName" >>> getChildren >>> getText -< mitogeneticcode + returnA -< TaxGenCode { + geneticCodeId = read _mgcId :: Int, + abbreviation = Nothing, + geneCodeName = _mgcName, + cde = [], + starts = [] + } + +parseTaxonLineageEx :: ArrowXml a => a XmlTree [LineageTaxon] +parseTaxonLineageEx = getChildren >>> atTag "LineageEx" >>> + proc taxonLineageEx -> do + _lineageEx <- listA parseLineageTaxon -< taxonLineageEx + returnA -< _lineageEx + +parseLineageTaxon :: ArrowXml a => a XmlTree LineageTaxon +parseLineageTaxon = getChildren >>> atTag "Taxon" >>> + proc lineageTaxon -> do + _lineageTaxId <- atTag "TaxId" >>> getChildren >>> getText -< lineageTaxon + _lineageScienticName <- atTag "ScientificName" >>> getChildren >>> getText -< lineageTaxon + _lineageRank <- atTag "Rank" >>> getChildren >>> getText -< lineageTaxon + returnA -< LineageTaxon { + lineageTaxId = read _lineageTaxId :: Int, + lineageScienticName = _lineageScienticName, + lineageRank = read _lineageRank :: Rank + } + +-- | Read entrez fetch for taxonomy database into a simplyfied datatype +-- Result of e.g: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=1406860 +readEntrezSimpleTaxons :: String -> [SimpleTaxon] +readEntrezSimpleTaxons = runLA (xreadDoc >>> parseEntrezSimpleTaxons) + +parseEntrezSimpleTaxons :: ArrowXml a => a XmlTree SimpleTaxon +parseEntrezSimpleTaxons = getChildren >>> atTag "Taxon" >>> + proc entrezSimpleTaxon -> do + simple_TaxId <- atTag "TaxId" >>> getChildren >>> getText -< entrezSimpleTaxon + simple_ScientificName <- atTag "ScientificName" >>> getChildren >>> getText -< entrezSimpleTaxon + simple_ParentTaxId <- atTag "ParentTaxId" >>> getChildren >>> getText -< entrezSimpleTaxon + simple_Rank <- atTag "Rank" >>> getChildren >>> getText -< entrezSimpleTaxon + returnA -< SimpleTaxon { + simpleTaxId = read simple_TaxId :: Int, + simpleScientificName = TL.pack simple_ScientificName, + simpleParentTaxId = read simple_ParentTaxId :: Int, + simpleRank = read simple_Rank :: Rank + } + +readEntrezParentIds :: String -> [Int] +readEntrezParentIds = runLA (xreadDoc >>> parseEntrezParentTaxIds) + +parseEntrezParentTaxIds :: ArrowXml a => a XmlTree Int +parseEntrezParentTaxIds = getChildren >>> atTag "Taxon" >>> + proc entrezSimpleTaxon -> do + simple_ParentTaxId <- atTag "ParentTaxId" >>> getChildren >>> getText -< entrezSimpleTaxon + returnA -< read simple_ParentTaxId :: Int + +-- | Read entrez summary from internal haskell string +readEntrezSummaries :: String -> [EntrezSummary] +readEntrezSummaries = runLA (xreadDoc >>> parseEntrezSummaries) + +-- | Parse entrez summary result +parseEntrezSummaries :: ArrowXml a => a XmlTree EntrezSummary +parseEntrezSummaries = atTag "eSummaryResult" >>> + proc entrezSummary -> do + document_Summaries <- listA parseEntrezDocSums -< entrezSummary + returnA -< EntrezSummary { + documentSummaries = document_Summaries + } + +-- | +parseEntrezDocSums :: ArrowXml a => a XmlTree EntrezDocSum +parseEntrezDocSums = atTag "DocSum" >>> + proc entrezDocSum -> do + summary_Id <- atTag "Id" >>> getChildren >>> getText -< entrezDocSum + summary_Items <- listA parseSummaryItems -< entrezDocSum + returnA -< EntrezDocSum { + summaryId = summary_Id, + summaryItems = summary_Items + } + +-- | +parseSummaryItems :: ArrowXml a => a XmlTree SummaryItem +parseSummaryItems = atTag "Item" >>> + proc summaryItem -> do + item_Name <- getAttrValue "Name" -< summaryItem + item_Type <- getAttrValue "Type" -< summaryItem + item_Content <- getText <<< getChildren -< summaryItem + returnA -< SummaryItem { + itemName = item_Name, + itemType = item_Type, + itemContent = item_Content + } + +-- | Read entrez summary from internal haskell string +readEntrezSearch :: String -> [EntrezSearch] +readEntrezSearch = runLA (xreadDoc >>> parseEntrezSearch) + +-- | Parse entrez search result +parseEntrezSearch :: ArrowXml a => a XmlTree EntrezSearch +parseEntrezSearch = atTag "eSearchResult" >>> + proc entrezSearch -> do + _count <- atTag "Count" >>> getChildren >>> getText -< entrezSearch + _retMax <- atTag "RetMax" >>> getChildren >>> getText -< entrezSearch + _retStart <- atTag "RetStart" >>> getChildren >>> getText -< entrezSearch + _searchIds <- atTag "IdList" >>> listA parseSearchId -< entrezSearch + _translationStack <- listA parseTranslationStack -< entrezSearch + _queryTranslation <- atTag "QueryTranslation" >>> getChildren >>> getText -< entrezSearch + returnA -< EntrezSearch { + count = readInt _count, + retMax = readInt _retMax, + retStart = readInt _retStart, + searchIds = _searchIds, + translationStack = _translationStack, + queryTranslation = _queryTranslation + } + +-- | Parse entrez TranslationStack +parseSearchId :: ArrowXml a => a XmlTree Int +parseSearchId = atTag "Id" >>> + proc entrezSearchId -> do + searchId <- getChildren >>> getText -< entrezSearchId + returnA -< (readInt searchId) + +-- | Parse entrez TranslationStack +parseTranslationStack :: ArrowXml a => a XmlTree TranslationStack +parseTranslationStack = atTag "TranslationStack" >>> + proc entrezTranslationStack -> do + _termSets <- listA parseTermSet -< entrezTranslationStack + _operation <- atTag "OP" >>> getChildren >>> getText -< entrezTranslationStack + returnA -< TranslationStack { + termSets = _termSets, + operation = _operation + } + +-- | Parse entrez TermSet +parseTermSet :: ArrowXml a => a XmlTree TermSet +parseTermSet = atTag "TermSet" >>> + proc entrezTermSet -> do + _term <- atTag "Term" >>> getChildren >>> getText -< entrezTermSet + _field <- atTag "Field" >>> getChildren >>> getText -< entrezTermSet + _termCount <- atTag "Count" >>> getChildren >>> getText -< entrezTermSet + _explode <- atTag "Explode" >>> getChildren >>> getText -< entrezTermSet + returnA -< TermSet { + term = _term, + field = _field, + termCount = readInt _termCount, + explode = _explode + } + +-- | Read entrez summary from internal haskell string +readEntrezGeneSummaries :: String -> [EntrezGeneSummary] +readEntrezGeneSummaries = runLA (xreadDoc >>> parseEntrezGeneSummaries) + +-- | Parse entrez summary result +parseEntrezGeneSummaries :: ArrowXml a => a XmlTree EntrezGeneSummary +parseEntrezGeneSummaries = atTag "eSummaryResult" >>> getChildren >>> atTag "DocumentSummarySet" >>> + proc entrezSummary -> do + _geneSummaries <- listA parseEntrezGeneDocSums -< entrezSummary + returnA -< EntrezGeneSummary { + geneSummaries = _geneSummaries + } + +-- | +parseEntrezGeneDocSums :: ArrowXml a => a XmlTree EntrezGeneDocSummary +parseEntrezGeneDocSums = atTag "DocumentSummary" >>> + proc entrezDocSum -> do + _geneId <- atTag "Name" >>> getChildren >>> getText -< entrezDocSum + _geneName <- atTag "Description" >>> getChildren >>> getText -< entrezDocSum + _geneStatus <- atTag "Status" >>> getChildren >>> getText -< entrezDocSum + _geneCurrentID <- atTag "CurrentID" >>> getChildren >>> getText -< entrezDocSum + _geneGeneticSource <- atTag "GeneticSource" >>> getChildren >>> getText -< entrezDocSum + _geneOtherAliases <- atTag "OtherAliases" >>> getChildren >>> getText -< entrezDocSum + _geneGenomicInfo <- parseEntrezGenomicInfo -< entrezDocSum + returnA -< EntrezGeneDocSummary { + geneId = _geneId, + geneName = _geneName, + geneStatus = _geneStatus, + geneCurrentID = _geneCurrentID, + geneGeneticSource = _geneGeneticSource, + geneOtherAliases = _geneOtherAliases, + geneGenomicInfo = _geneGenomicInfo + } + +parseEntrezGenomicInfo :: ArrowXml a => a XmlTree EntrezGenomicInfo +parseEntrezGenomicInfo = atTag "GenomicInfo" >>> getChildren >>> atTag "GenomicInfoType" >>> + proc entrezGenomicInfo -> do + _chrAccVer <- atTag "ChrAccVer" >>> getChildren >>> getText -< entrezGenomicInfo + _chrStart <- atTag "ChrStart" >>> getChildren >>> getText -< entrezGenomicInfo + _chrStop <- atTag "ChrStop" >>> getChildren >>> getText -< entrezGenomicInfo + _exonCount <- atTag "ExonCount" >>> getChildren >>> getText -< entrezGenomicInfo + returnA -< EntrezGenomicInfo { + chrAccVer = _chrAccVer, + chrStart = readInt _chrStart, + chrStop = readInt _chrStop, + exonCount = readInt _exonCount + } + + +-- | gets all subtrees with the specified tag name +atTag :: ArrowXml a => String -> a XmlTree XmlTree +atTag tag = deep (isElem >>> hasName tag) + +--------------------------------------- +-- Retrieval functions + +-- | Retrieve sequence for gene symbol (e.g. yhfA) from accession number (e.g. NC_000913.3) and if available entrez registration (toolname,devemail) +retrieveGeneSymbolFasta :: String -> String -> Maybe (String,String) -> IO String +retrieveGeneSymbolFasta genesymbol accession registrationInfo = do + let query1 = EntrezHTTPQuery (Just "esearch") (Just "gene") ("term=" ++ genesymbol ++ urlEncode ("[Gene Name] AND " ++ accession ++ "[Nucleotide Accession]")) + --print query1 + uniqueidresponse <- entrezHTTP query1 + --print uniqueidresponse + let uniqueid = head (searchIds (head (readEntrezSearch uniqueidresponse))) + let query2 = EntrezHTTPQuery (Just "esummary") (Just "gene") ("id=" ++ show uniqueid) + summaryresponse <- entrezHTTP query2 + --print summaryresponse + let parsedSummary = head (geneSummaries (head (readEntrezGeneSummaries summaryresponse))) + let accessionVersion = chrAccVer (geneGenomicInfo parsedSummary) + let seqStart = chrStart (geneGenomicInfo parsedSummary) + let seqStop = chrStop (geneGenomicInfo parsedSummary) + let strand = convertCoordinatesToStrand seqStart seqStop + fetchNucleotideString accessionVersion seqStart seqStop strand registrationInfo + + +-- | Fetches sequence strings from the nucleotide database. nucleotideId can be a NCBI accession number or gene id. +-- Strand is 1 in case of plus strand (forward) or 2 minus (reverse) strand, the setStrand function can be used for conversion. +fetchNucleotideString :: String -> Int -> Int -> Int -> Maybe (String,String) -> IO String +fetchNucleotideString nucleotideId seqStart seqStop strand maybeRegistrationInfo = do + let registrationInfo = maybeBuildRegistration maybeRegistrationInfo + let program' = Just "efetch" + let database' = Just "nucleotide" + let query' = "id=" ++ nucleotideId ++ "&seq_start=" ++ show seqStart ++ "&seq_stop=" ++ show seqStop ++ "&rettype=fasta" ++ "&strand=" ++ show strand ++ registrationInfo + let entrezQuery = EntrezHTTPQuery program' database' query' + entrezHTTP entrezQuery + +convertCoordinatesToStrand :: Int -> Int -> Int +convertCoordinatesToStrand start end + | start <= end = 1 + | otherwise = 2 + +setStrand :: String -> Int +setStrand strandString + | strandString == "+" = 1 + | strandString == "-" = 2 + | strandString == "forward" = 1 + | strandString == "reverse" = 2 + | strandString == "Forward" = 1 + | strandString == "Reverse" = 2 + | strandString == "plus" = 1 + | strandString == "false" = 2 + | strandString == "Plus" = 1 + | strandString == "False" = 2 + | otherwise = 1 + +readInt :: String -> Int +readInt = read + +-- | Builds Entrez registration String if present +maybeBuildRegistration :: Maybe (String,String) -> String +maybeBuildRegistration maybeRegistration + | isJust maybeRegistration = buildRegistration toolname developeremail + | otherwise = "" + where registration = fromJust maybeRegistration + toolname = fst registration + developeremail = snd registration + +-- | Builds Entrez registration String that has to be appended to query key +buildRegistration :: String -> String -> String +buildRegistration toolname developeremail = "&tool=" ++ toolname ++ "&email=" ++ developeremail diff --git a/Biobase/Entrez/HTTPData.hs b/Biobase/Entrez/HTTPData.hs new file mode 100644 --- /dev/null +++ b/Biobase/Entrez/HTTPData.hs @@ -0,0 +1,73 @@ +-- | Data structures for Entrez HTTP queries + +module Biobase.Entrez.HTTPData where + +-- | Input datastructure for EntrezHTTP. Program is the selected eutility (e.g efetch, esearch), +-- database is the selected Entrez database (nucleotide) and query the query string. +data EntrezHTTPQuery = EntrezHTTPQuery + { program :: Maybe String + , database :: Maybe String + , query :: String + } + deriving (Show, Eq) + +-- | Data structure for Entrez summary result +newtype EntrezSummary = EntrezSummary + { documentSummaries :: [EntrezDocSum]} + deriving (Show, Eq) + +data EntrezDocSum = EntrezDocSum + { summaryId :: String + , summaryItems :: [SummaryItem]} + deriving (Show, Eq) + +data SummaryItem = SummaryItem + { itemName :: String + , itemType :: String + , itemContent :: String} + deriving (Show, Eq) + +-- | Gene doc summary +newtype EntrezGeneSummary = EntrezGeneSummary + { geneSummaries :: [EntrezGeneDocSummary]} + deriving (Show, Eq) + +data EntrezGeneDocSummary = EntrezGeneDocSummary + { geneId :: String + , geneName :: String + , geneStatus :: String + , geneCurrentID :: String + , geneGeneticSource :: String + , geneOtherAliases :: String + , geneGenomicInfo :: EntrezGenomicInfo} + deriving (Show, Eq) + +data EntrezGenomicInfo = EntrezGenomicInfo + { chrAccVer :: String + , chrStart :: Int + , chrStop :: Int + , exonCount :: Int + } + deriving (Show, Eq) + +-- | Data structure for Entrez search result +data EntrezSearch = EntrezSearch + { count :: Int + , retMax :: Int + , retStart :: Int + , searchIds :: [Int] + , translationStack :: [TranslationStack] + , queryTranslation :: String} + deriving (Show, Eq) + +data TranslationStack = TranslationStack + { termSets :: [TermSet] + , operation :: String} + deriving (Show, Eq) + +data TermSet = TermSet + { term :: String + , field :: String + , termCount :: Int + , explode :: String} + deriving (Show, Eq) diff --git a/BiobaseHTTP.cabal b/BiobaseHTTP.cabal new file mode 100644 --- /dev/null +++ b/BiobaseHTTP.cabal @@ -0,0 +1,43 @@ +name: BiobaseHTTP +version: 1.1.0 +synopsis: Libary to interface with the Bioinformatics HTTP services - Entrez Ensembl +description: BiobaseHTTP provides functions to interface the Bioinformatics REST services - Entrez Ensembl + . + NCBI Entrez provides multiple different databases and eutils. + . + For more information on Entrez refer to: . + . + Information on the webservice can be found at: . + If you plan to include the library in a tool, register it as explained . + . + Information on ENSEMBL genomes API can be found here: . + . + BiobaseHTTP is the successor of the deprecated EntrezHTTP library. +license: GPL-3 +license-file: LICENSE +author: Florian Eggenhofer +maintainer: egg@informatik.uni-freiburg.de +copyright: Florian Eggenhofer +homepage: https://github.com/eggzilla/BiobaseHTTP +category: Bioinformatics +build-type: Simple +cabal-version: >=1.8 +Tested-With: GHC == 8.4.3 + +Extra-Source-Files: + README.md changelog + +source-repository head + type: git + location: https://github.com/eggzilla/BiobaseHTTP + +source-repository this + type: darcs + location: https://github.com/eggzilla/BiobaseHTTP/tree/1.1.0 + tag: 1.1.0 + +library + exposed-modules: Biobase.Entrez.HTTP, Biobase.Entrez.HTTPData, Biobase.Ensembl.HTTP + ghc-options: -Wall + build-depends: base >=4.5 && <5, transformers, bytestring, conduit, HTTP, http-conduit, hxt, network, mtl, Taxonomy>=1.0.3, text, aeson, either-unwrap, BiobaseEnsembl + hs-source-dirs: . diff --git a/LICENSE b/LICENSE new file mode 100644 --- /dev/null +++ b/LICENSE @@ -0,0 +1,675 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + 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. 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But first, please read +. + diff --git a/README.md b/README.md new file mode 100644 --- /dev/null +++ b/README.md @@ -0,0 +1,17 @@ +BiobaseHTTP +[![Hackage](https://img.shields.io/hackage/v/BiobaseHTTP.svg)](https://hackage.haskell.org/package/BiobaseHTTP) [![Build Status](https://travis-ci.org/eggzilla/BiobaseHTTP.svg?branch=master)](https://travis-ci.org/eggzilla/BiobaseHTTP) +========= + +BiobaseHTTP provides functions to interface the Bioinformatics REST services - Entrez Ensembl. + +NCBI Entrez provides multiple different databases and eutils. + +For more information on Entrez refer to: [Entrez](http://www.ncbi.nlm.nih.gov/gquery/). + +Information on the webservice can be found at: [NCBI books](http://www.ncbi.nlm.nih.gov/books/NBK25497/). + +Information on ENSEMBL genomes API can be found here: [Ensembl Genomes](http://rest.ensemblgenomes.org/). + +If you plan to include the library in a tool, register it as explained [here](http://www.ncbi.nlm.nih.gov/books/NBK25497/#chapter2.Usage_Guidelines_and_Requiremen). + +BiobaseHTTP is the successor of the deprecated EntrezHTTP library. 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/changelog b/changelog new file mode 100644 --- /dev/null +++ b/changelog @@ -0,0 +1,17 @@ +-*-change-log-*- +1.1.0 Florian Eggenhofer 12 December 2018 + * Changed library name to BiobaseHTTP + * Now using Biobase libraries + * Added functionality for Ensembl Genomes API requests +1.0.4 Florian Eggenhofer 10. August 2017 + * Updated version constraints for Taxonomy +1.0.3 Florian Eggenhofer 12. November 2016 + * Default NCBI URL now uses HTTPS +1.0.2 Florian Eggenhofer 23. October 2016 + * Now compatible with GHC 8.0 + * Travis testing for GHC 7.6 - GHC 8.0 +1.0.1 Florian Eggenhofer 5. January 2016 + * Fixed version constraints, added changelog +1.0.0 Florian Eggenhofer 11.September 2015 + * Initial version +