fasta 0.5.1.5 → 0.5.2.0

raw patch · 4 files changed

+30/−10 lines, 4 filesdep ~parsecPVP ok

version bump matches the API change (PVP)

Dependency ranges changed: parsec

API changes (from Hackage documentation)

Files

fasta.cabal +2/−2
src/Data/Fasta/String/Parse.hs +6/−0
src/Data/Fasta/Text/Lazy/Parse.hs +11/−4
src/Data/Fasta/Text/Parse.hs +11/−4

fasta.cabal view

@@ -10,7 +10,7 @@ -- PVP summary:      +-+------- breaking API changes --                   | | +----- non-breaking API additions --                   | | | +--- code changes with no API change-version:             0.5.1.5+version:             0.5.2.0  -- A short (one-line) description of the package. synopsis:            A simple, mindless parser for fasta files.@@ -65,7 +65,7 @@      -- Other library packages from which modules are imported.   build-depends:       base >=4.6 && <4.9,-                       parsec >=3.1.0 && <4.0,+                       parsec >=3.1 && <4.0,                        text >=1.1.0 && <1.4,                        containers >= 0.5 && <0.6,                        split >= 0.2 && <0.3

src/Data/Fasta/String/Parse.hs view

@@ -82,6 +82,12 @@   where     noN = map (\y -> if (y /= 'N' && y /= 'n') then y else '-') +-- | Remove Ns from a sequence+removeN :: FastaSequence -> FastaSequence+removeN x = x { fastaSeq = noN . fastaSeq $ x }+  where+    noN = map (\y -> if (y /= 'N' && y /= 'n') then y else '-')+ -- | Remove Ns from a collection of CLIP fasta sequences removeCLIPNs :: CloneMap -> CloneMap removeCLIPNs = M.fromList . map remove . M.toList

src/Data/Fasta/Text/Lazy/Parse.hs view

@@ -6,6 +6,7 @@ -}  {-# LANGUAGE OverloadedStrings #-}+{-# LANGUAGE BangPatterns #-}  module Data.Fasta.Text.Lazy.Parse ( parseFasta                                   , parseCLIPFasta@@ -15,7 +16,7 @@ -- Built-in import Data.Char import Control.Monad (void)-import qualified Data.Map as M+import qualified Data.Map.Strict as M import Text.Parsec import Text.Parsec.Text.Lazy import qualified Data.Text.Lazy as T@@ -71,7 +72,7 @@ -- | Parse a CLIP fasta file into lazy text sequences parseCLIPFasta :: T.Text -> CloneMap parseCLIPFasta = M.fromList-               . map (\(x, (y, z)) -> ((x, y), z))+               . map (\(!x, (!y, !z)) -> ((x, y), z))                . zip [0..]                . eToV                . parse fastaCLIPFile "error"@@ -85,10 +86,16 @@   where     noN = T.map (\y -> if (y /= 'N' && y /= 'n') then y else '-') +-- | Remove Ns from a sequence+removeN :: FastaSequence -> FastaSequence+removeN x = x { fastaSeq = noN . fastaSeq $ x }+  where+    noN = T.map (\y -> if (y /= 'N' && y /= 'n') then y else '-')+ -- | Remove Ns from a collection of CLIP fasta sequences removeCLIPNs :: CloneMap -> CloneMap removeCLIPNs = M.fromList . map remove . M.toList   where-    remove   ((x, y), z)    = ((x, newSeq y), map newSeq z)-    newSeq x = x { fastaSeq = noN . fastaSeq $ x }+    remove   ((!x, !y), !z)    = ((x, newSeq y), map newSeq z)+    newSeq !x = x { fastaSeq = noN . fastaSeq $ x }     noN = T.map (\y -> if (y /= 'N' && y /= 'n') then y else '-')

src/Data/Fasta/Text/Parse.hs view

@@ -6,6 +6,7 @@ -}  {-# LANGUAGE OverloadedStrings #-}+{-# LANGUAGE BangPatterns #-}  module Data.Fasta.Text.Parse ( parseFasta                              , parseCLIPFasta@@ -14,7 +15,7 @@  -- Built-in import Data.Char-import qualified Data.Map as M+import qualified Data.Map.Strict as M import Control.Monad (void) import Text.Parsec import Text.Parsec.Text@@ -72,7 +73,7 @@ -- | Parse a CLIP fasta file into text sequences parseCLIPFasta :: T.Text -> CloneMap parseCLIPFasta = M.fromList-               . map (\(x, (y, z)) -> ((x, y), z))+               . map (\(!x, (!y, !z)) -> ((x, y), z))                . zip [0..]                . eToV                . parse fastaCLIPFile "error"@@ -86,10 +87,16 @@   where     noN = T.map (\y -> if (y /= 'N' && y /= 'n') then y else '-') +-- | Remove Ns from a sequence+removeN :: FastaSequence -> FastaSequence+removeN x = x { fastaSeq = noN . fastaSeq $ x }+  where+    noN = T.map (\y -> if (y /= 'N' && y /= 'n') then y else '-')+ -- | Remove Ns from a collection of CLIP fasta sequences removeCLIPNs :: CloneMap -> CloneMap removeCLIPNs = M.fromList . map remove . M.toList   where-    remove   ((x, y), z)    = ((x, newSeq y), map newSeq z)-    newSeq x = x { fastaSeq = noN . fastaSeq $ x }+    remove   ((!x, !y), !z)    = ((x, newSeq y), map newSeq z)+    newSeq !x = x { fastaSeq = noN . fastaSeq $ x }     noN = T.map (\y -> if (y /= 'N' && y /= 'n') then y else '-')