cobot-io 0.1.3.18 → 0.1.3.19

raw patch · 5 files changed

+16/−7 lines, 5 filesPVP: minor bump suggested

API additions: PVP suggests at least a minor version bump

API changes (from Hackage documentation)

+ Bio.FASTA: fastaLine :: ParsableFastaToken a => (Char -> Bool) -> Parser [a]

+ Bio.FASTA: modificationP :: Parser Modification

+ Bio.FASTA.Parser: fastaLine :: ParsableFastaToken a => (Char -> Bool) -> Parser [a]

+ Bio.FASTA.Parser: modificationP :: Parser Modification

+ Bio.FASTA.Type: instance GHC.Classes.Ord Bio.FASTA.Type.Modification

+ Bio.FASTA.Type: instance GHC.Generics.Generic Bio.FASTA.Type.ModItem

+ Bio.FASTA.Type: instance GHC.Generics.Generic Bio.FASTA.Type.Modification

Files

ChangeLog.md +4/−0
cobot-io.cabal +2/−2
src/Bio/FASTA.hs +2/−0
src/Bio/FASTA/Parser.hs +5/−3
src/Bio/FASTA/Type.hs +3/−2

ChangeLog.md view

@@ -2,6 +2,10 @@  ## [Unreleased] +## [0.1.3.19] - 2021-04-30+### Changed +- Exports and instances for Biosset. + ## [0.1.3.18] - 2021-03-09 ### Fixed - Lowercase insertion code parsing in PDB.

cobot-io.cabal view

@@ -4,10 +4,10 @@ -- -- see: https://github.com/sol/hpack ----- hash: fe5f3bd32c503a44c34349ccfa5bf4ef5ec52540df5c2ce4637127a0b33394df+-- hash: 543c70618887552cd7833594bf0cb48d233a34c25568ca9cd5ddcf6a3914a5c5  name:           cobot-io-version:        0.1.3.18+version:        0.1.3.19 synopsis:       Biological data file formats and IO description:    Please see the README on GitHub at <https://github.com/biocad/cobot-io#readme> category:       Bio

src/Bio/FASTA.hs view

@@ -7,6 +7,8 @@   , toFile   , fastaP   , fastaPGeneric+  , fastaLine+  , modificationP   ) where  import Control.Monad.IO.Class (MonadIO, liftIO)

src/Bio/FASTA/Parser.hs view

@@ -3,6 +3,8 @@ module Bio.FASTA.Parser   ( fastaP   , fastaPGeneric+  , fastaLine +  , modificationP   ) where  import Bio.FASTA.Type       (Fasta, FastaItem (..), ModItem (..), Modification (..),@@ -37,10 +39,10 @@ seqName = strip <$> (char '>' *> tabs *> takeWhile (`notElem` ['\n', '\r']) <* tabs <* eol)  fastaSeq :: ParsableFastaToken a => (Char -> Bool) -> Parser (BareSequence a)-fastaSeq predicate = bareSequence . mconcat <$> many' (line predicate)+fastaSeq predicate = bareSequence . mconcat <$> many' (fastaLine predicate) -line :: ParsableFastaToken a => (Char -> Bool) -> Parser [a]-line predicate = concat <$> many1' (many1' (parseToken predicate) <* many' (char ' ')) <* eol+fastaLine :: ParsableFastaToken a => (Char -> Bool) -> Parser [a]+fastaLine predicate = concat <$> many1' (many1' (parseToken predicate) <* many' (char ' ')) <* eol  eol :: Parser () eol = tabs *> choice [slashN, endOfInput]

src/Bio/FASTA/Type.hs view

@@ -10,6 +10,7 @@ import Bio.Sequence         (BareSequence) import Data.Attoparsec.Text (Parser) import Data.Text            (Text)+import GHC.Generics         (Generic)  -- | Type alias for FASTA file. --  satisfies the following format : >(\s|\t)*[^\n\r]+(\s|\t)*(\n|\r)*((\w|\s)(\n|\r)*)*@@ -33,7 +34,7 @@ data ModItem   = Mod Modification   | Letter Char-  deriving (Eq, Show)+  deriving (Eq, Show, Generic)  data Modification   = Mod_A_Star@@ -124,7 +125,7 @@   | Mod_TTC   | Mod_TTT   | Unknown String-  deriving (Eq, Show)+  deriving (Eq, Show, Ord, Generic)  modificationToString :: Modification -> String modificationToString Mod_A_Star   = "[A*]"