| Safe Haskell | None |
|---|---|
| Language | Haskell98 |
Bio.Taxonomy
Description
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 "pathto/dotdirectory" subtree
- module Bio.TaxonomyData
- readTaxonomy :: String -> IO (Either ParseError (Gr SimpleTaxon Double))
- readNamedTaxonomy :: String -> IO (Either ParseError (Gr SimpleTaxon Double))
- parseTaxonomy :: String -> Either ParseError (Gr SimpleTaxon Double)
- parseNCBITaxCitations :: String -> Either ParseError [TaxCitation]
- readNCBITaxCitations :: String -> IO (Either ParseError [TaxCitation])
- parseNCBITaxDelNodes :: String -> Either ParseError [TaxDelNode]
- readNCBITaxDelNodes :: String -> IO (Either ParseError [TaxDelNode])
- parseNCBITaxDivisions :: String -> Either ParseError [TaxDivision]
- readNCBITaxDivisions :: String -> IO (Either ParseError [TaxDivision])
- parseNCBITaxGenCodes :: String -> Either ParseError [TaxGenCode]
- readNCBITaxGenCodes :: String -> IO (Either ParseError [TaxGenCode])
- parseNCBITaxMergedNodes :: String -> Either ParseError [TaxMergedNode]
- readNCBITaxMergedNodes :: String -> IO (Either ParseError [TaxMergedNode])
- parseNCBITaxNames :: String -> Either ParseError [TaxName]
- readNCBITaxNames :: String -> IO (Either ParseError [TaxName])
- parseNCBITaxNodes :: String -> Either ParseError TaxNode
- readNCBITaxNodes :: String -> IO (Either ParseError [TaxNode])
- parseNCBISimpleTaxons :: String -> Either ParseError SimpleTaxon
- readNCBISimpleTaxons :: String -> IO (Either ParseError [SimpleTaxon])
- readNCBITaxonomyDatabase :: String -> IO (Either [String] NCBITaxDump)
- compareSubTrees :: [Gr SimpleTaxon Double] -> (Int, Gr CompareTaxon Double)
- extractTaxonomySubTreebyLevel :: [Node] -> Gr SimpleTaxon Double -> Maybe Int -> Gr SimpleTaxon Double
- extractTaxonomySubTreebyLevelNew :: [Node] -> Gr SimpleTaxon Double -> Maybe Int -> Gr SimpleTaxon Double
- extractTaxonomySubTreebyRank :: [Node] -> Gr SimpleTaxon Double -> Maybe Rank -> Gr SimpleTaxon Double
- safeNodePath :: Maybe Node -> Gr SimpleTaxon Double -> Maybe Node -> Either String Path
- getParentbyRank :: Node -> Gr SimpleTaxon Double -> Maybe Rank -> Maybe (Node, SimpleTaxon)
- drawTaxonomyComparison :: Bool -> (Int, Gr CompareTaxon Double) -> String
- drawTaxonomy :: Bool -> Gr SimpleTaxon Double -> String
- writeTree :: String -> String -> Bool -> Gr SimpleTaxon Double -> IO ()
- writeDotTree :: String -> Bool -> Gr SimpleTaxon Double -> IO ()
- writeJsonTree :: String -> Gr SimpleTaxon Double -> IO ()
Datatypes
module Bio.TaxonomyData
Parsing
readTaxonomy :: String -> IO (Either ParseError (Gr SimpleTaxon Double)) Source #
NCBI taxonomy dump nodes and names in the input directory path are parsed and a SimpleTaxon tree is generated.
readNamedTaxonomy :: String -> IO (Either ParseError (Gr SimpleTaxon Double)) Source #
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.
parseTaxonomy :: String -> Either ParseError (Gr SimpleTaxon Double) Source #
NCBI taxonomy dump nodes and names in the input directory path are parsed and a SimpleTaxon tree is generated.
parseNCBITaxCitations :: String -> Either ParseError [TaxCitation] Source #
parse NCBITaxCitations from input string
readNCBITaxCitations :: String -> IO (Either ParseError [TaxCitation]) Source #
parse NCBITaxCitations from input filePath
parseNCBITaxDelNodes :: String -> Either ParseError [TaxDelNode] Source #
parse NCBITaxDelNodes from input string
readNCBITaxDelNodes :: String -> IO (Either ParseError [TaxDelNode]) Source #
parse NCBITaxDelNodes from input filePath
parseNCBITaxDivisions :: String -> Either ParseError [TaxDivision] Source #
parse NCBITaxDivisons from input string
readNCBITaxDivisions :: String -> IO (Either ParseError [TaxDivision]) Source #
parse NCBITaxDivisons from input filePath
parseNCBITaxGenCodes :: String -> Either ParseError [TaxGenCode] Source #
parse NCBITaxGenCodes from input string
readNCBITaxGenCodes :: String -> IO (Either ParseError [TaxGenCode]) Source #
parse NCBITaxGenCodes from input filePath
parseNCBITaxMergedNodes :: String -> Either ParseError [TaxMergedNode] Source #
parse NCBITaxMergedNodes from input string
readNCBITaxMergedNodes :: String -> IO (Either ParseError [TaxMergedNode]) Source #
parse NCBITaxMergedNodes from input filePath
parseNCBITaxNames :: String -> Either ParseError [TaxName] Source #
parse NCBITaxNames from input string
readNCBITaxNames :: String -> IO (Either ParseError [TaxName]) Source #
parse NCBITaxNames from input filePath
parseNCBITaxNodes :: String -> Either ParseError TaxNode Source #
parse NCBITaxNames from input string
readNCBITaxNodes :: String -> IO (Either ParseError [TaxNode]) Source #
parse NCBITaxCitations from input filePath
parseNCBISimpleTaxons :: String -> Either ParseError SimpleTaxon Source #
parse NCBISimpleTaxNames from input string
readNCBISimpleTaxons :: String -> IO (Either ParseError [SimpleTaxon]) Source #
parse NCBITaxCitations from input filePath
readNCBITaxonomyDatabase :: String -> IO (Either [String] NCBITaxDump) Source #
Parse the input as NCBITax datatype
Processing
compareSubTrees :: [Gr SimpleTaxon Double] -> (Int, Gr CompareTaxon Double) Source #
Extract a subtree correpsonding to input node paths to root. Only nodes in level number distance to root are included. Used in Ids2TreeCompare tool.
extractTaxonomySubTreebyLevel :: [Node] -> Gr SimpleTaxon Double -> Maybe Int -> Gr SimpleTaxon Double Source #
Extract a subtree corresponding to input node paths to root. Only nodes in level number distance to root are included. Used in Ids2Tree tool.
extractTaxonomySubTreebyLevelNew :: [Node] -> Gr SimpleTaxon Double -> Maybe Int -> Gr SimpleTaxon Double Source #
Extract a subtree corresponding to input node paths to root. Only nodes in level number distance to root are included. Used in Ids2Tree tool.
extractTaxonomySubTreebyRank :: [Node] -> Gr SimpleTaxon Double -> Maybe Rank -> Gr SimpleTaxon Double Source #
Extract a subtree corresponding to input node paths to root. If a Rank is provided, all node that are less or equal are omitted
safeNodePath :: Maybe Node -> Gr SimpleTaxon Double -> Maybe Node -> Either String Path Source #
Returns path between 2 maybe nodes. Used in TreeDistance tool.
getParentbyRank :: Node -> Gr SimpleTaxon Double -> Maybe Rank -> Maybe (Node, SimpleTaxon) Source #
Extract parent node with specified Rank
Visualization
drawTaxonomyComparison :: Bool -> (Int, Gr CompareTaxon Double) -> String Source #
Draw tree comparison graph in dot format. Used in Ids2TreeCompare tool.
drawTaxonomy :: Bool -> Gr SimpleTaxon Double -> String Source #
Draw graph in dot format. Used in Ids2Tree tool.
writeTree :: String -> String -> Bool -> Gr SimpleTaxon Double -> IO () Source #
Write tree representation either as dot or json to provided file path
writeDotTree :: String -> Bool -> Gr SimpleTaxon Double -> IO () Source #
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.
writeJsonTree :: String -> Gr SimpleTaxon Double -> IO () Source #
Write tree representation as json to provided file path. You can visualize the result for example with 3Djs.