bioinformatics-toolkit 0.3.0 → 0.3.1

raw patch · 11 files changed

+30/−96 lines, 11 files

Files

• LICENSE +1/−1
• bioinformatics-toolkit.cabal +1/−1
• src/Bio/Data/Bed.hs +0/−12
• src/Bio/Data/Fasta.hs +3/−17
• src/Bio/GO/GREAT.hs +2/−4
• src/Bio/GO/Parser.hs +8/−8
• src/Bio/RealWorld/ENCODE.hs +2/−15
• src/Bio/RealWorld/UCSC.hs +0/−13
• src/Bio/Utils/Functions.hs +0/−12
• src/Bio/Utils/Misc.hs +4/−4
• src/Bio/Utils/Overlap.hs +9/−9

@@ -1,6 +1,6 @@ The MIT License (MIT) -Copyright (c) 2014 Kai Zhang+Copyright (c) 2014-2016 Kai Zhang  Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal

@@ -1,5 +1,5 @@ name:                bioinformatics-toolkit-version:             0.3.0+version:             0.3.1 synopsis:            A collection of bioinformatics tools description:         A collection of bioinformatics tools license:             MIT

@@ -1,17 +1,5 @@ {-# LANGUAGE OverloadedStrings #-} {-# LANGUAGE FlexibleContexts #-}------------------------------------------------------------------------------------ |--- Module      :  $Header$--- Copyright   :  (c) 2014 Kai Zhang--- License     :  MIT---- Maintainer  :  kai@kzhang.org--- Stability   :  experimental--- Portability :  portable---- functions for processing BED files---------------------------------------------------------------------------------  module Bio.Data.Bed     ( BEDLike(..)

@@ -1,18 +1,6 @@ {-# LANGUAGE FlexibleInstances #-} {-# LANGUAGE UndecidableInstances #-}------------------------------------------------------------------------------------ |--- Module      :  $Header$--- Copyright   :  (c) 2014 Kai Zhang--- License     :  MIT --- Maintainer  :  kai@kzhang.org--- Stability   :  experimental--- Portability :  portable---- Functions for processing Fasta files---------------------------------------------------------------------------------- module Bio.Data.Fasta     ( FastaLike(..)     , fastaReader@@ -24,10 +12,9 @@ import Conduit  class FastaLike f where-    fromFastaRecord :: ( B.ByteString    -- ^ record header-                       , [B.ByteString]  -- ^ record body-                       )-                    -> f+    -- | Convert a FASTA record, consisting of a record header and a record body,+    -- to a specific data type+    fromFastaRecord :: (B.ByteString, [B.ByteString]) -> f      readFasta :: FilePath -> Source (ResourceT IO) f     readFasta fl = fastaReader fl =$= mapC fromFastaRecord@@ -35,7 +22,6 @@     -- | non-stream version, read whole file in memory     readFasta' :: FilePath -> IO [f]     readFasta' fl = runResourceT $ readFasta fl $$ sinkList---    writeFasta :: FilePath -> [f] -> IO ()     {-# MINIMAL fromFastaRecord #-}  instance BioSeq s a => FastaLike (s a) where

@@ -30,10 +30,8 @@ instance Default AssocRule where     def = BasalPlusExtension 5000 1000 1000000 -type Gene a = ( ( B.ByteString  -- ^ chromosome-              , Int           -- ^ tss-              , Bool          -- ^ is forward stranded-              ), a)+-- | A Gene consists of the chromosome name, TSS, strandness and an associated value.+type Gene a = ((B.ByteString, Int, Bool), a)  -- | given a gene list and the rule, compute the rulatory domain for each gene getRegulatoryDomains :: AssocRule -> [Gene a] -> [(BED3, a)]

@@ -4,16 +4,16 @@     , readOWLAsMap     ) where -import Control.Arrow ((&&&))+import           Control.Arrow              ((&&&)) import qualified Data.ByteString.Lazy.Char8 as L-import qualified Data.HashMap.Strict as M-import Data.Maybe-import qualified Data.Text as T-import Data.Text.Encoding (encodeUtf8)-import Text.XML.Expat.Proc-import Text.XML.Expat.Tree+import qualified Data.HashMap.Strict        as M+import           Data.Maybe+import qualified Data.Text                  as T+import           Data.Text.Encoding         (encodeUtf8)+import           Text.XML.Expat.Proc+import           Text.XML.Expat.Tree -import Bio.GO+import           Bio.GO  readOWL :: FilePath -> IO [GO] readOWL fl = do

@@ -1,18 +1,5 @@ {-# LANGUAGE OverloadedStrings #-}------------------------------------------------------------------------------------ |--- Module      :  $Header$--- Description :  Search and download data from ENCODE project--- Copyright   :  (c) Kai Zhang--- License     :  MIT --- Maintainer  :  kai@kzhang.org--- Stability   :  experimental--- Portability :  portable---- Search and download data from ENCODE project---------------------------------------------------------------------------------- module Bio.RealWorld.ENCODE     ( KeyWords(..)     , search@@ -53,8 +40,8 @@  import Bio.RealWorld.ID -data KeyWords = KeyWords (S.Seq String)  -- ^ terms-                         (S.Seq String)  -- ^ constraints+-- | Terms and constraints.+data KeyWords = KeyWords (S.Seq String) (S.Seq String)  instance Default KeyWords where     def = KeyWords S.empty $ S.fromList ["frame=object", "limit=all"]

@@ -1,17 +1,4 @@ {-# LANGUAGE OverloadedStrings #-}------------------------------------------------------------------------------------ |--- Module      :  $Header$--- Description :  Search and download data from ENCODE project--- Copyright   :  (c) Kai Zhang--- License     :  MIT---- Maintainer  :  kai@kzhang.org--- Stability   :  experimental--- Portability :  portable---- resources from UCSC---------------------------------------------------------------------------------  module Bio.RealWorld.UCSC     ( UCSCGene(..)

@@ -1,17 +1,5 @@ {-# LANGUAGE BangPatterns #-} {-# LANGUAGE FlexibleContexts #-}------------------------------------------------------------------------------------ |--- Module      :  $Header$--- Copyright   :  (c) 2014 Kai Zhang--- License     :  MIT---- Maintainer  :  kai@kzhang.org--- Stability   :  experimental--- Portability :  portable---- some useful functions---------------------------------------------------------------------------------  module Bio.Utils.Functions (       ihs

@@ -7,10 +7,10 @@     , binBySizeOverlap     ) where -import Data.ByteString.Char8 (ByteString)-import Data.ByteString.Lex.Fractional (readSigned, readExponential)-import Data.ByteString.Lex.Integral (readDecimal)-import Data.Maybe (fromMaybe)+import           Data.ByteString.Char8          (ByteString)+import           Data.ByteString.Lex.Fractional (readExponential, readSigned)+import           Data.ByteString.Lex.Integral   (readDecimal)+import           Data.Maybe                     (fromMaybe)  readInt :: ByteString -> Int readInt x = fst . fromMaybe errMsg . readSigned readDecimal $ x

@@ -4,16 +4,16 @@     , coverage     ) where -import qualified Data.ByteString.Char8 as B-import qualified Data.IntervalMap.Strict as IM-import qualified Data.HashMap.Strict as M-import qualified Data.Vector.Unboxed as V+import           Bio.Data.Bed+import           Conduit+import           Control.Monad+import qualified Data.ByteString.Char8       as B+import           Data.Function+import qualified Data.HashMap.Strict         as M+import qualified Data.IntervalMap.Strict     as IM+import           Data.List+import qualified Data.Vector.Unboxed         as V import qualified Data.Vector.Unboxed.Mutable as VM-import Data.List-import Data.Function-import Bio.Data.Bed-import Control.Monad-import Conduit  -- | convert lines of a BED file into a data structure - A hashmap of which the -- | chromosomes, and values are interval maps.