Version 0.1.3.19. Exports and instances for Biosset. (#54)

ChangeLog.md

@@ -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.

package.yaml

@@ -1,5 +1,5 @@
 name:                cobot-io
-version:             0.1.3.18
+version:             0.1.3.19
 github:              "biocad/cobot-io"
 license:             BSD3
 category:            Bio

src/Bio/FASTA.hs

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

src/Bio/FASTA/Parser.hs

@@ -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 :: Parser Text
 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

@@ -10,6 +10,7 @@ module Bio.FASTA.Type
 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 @@ class ParsableFastaToken a where
 data ModItem
   = Mod Modification
   | Letter Char
-  deriving (Eq, Show)
+  deriving (Eq, Show, Generic)
 
 data Modification
   = Mod_A_Star
@@ -124,7 +125,7 @@ data Modification
   | Mod_TTC
   | Mod_TTT
   | Unknown String
-  deriving (Eq, Show)
+  deriving (Eq, Show, Ord, Generic)
 
 modificationToString :: Modification -> String
 modificationToString Mod_A_Star   = "[A*]"