Version 0.1.4.2. Multiline props are supported. (#63)

biocad · Oct 14, 2021 · f7a953d · f7a953d
1 parent c44bde5
commit f7a953d
Show file tree

Hide file tree

Showing 5 changed files with 39 additions and 16 deletions.
diff --git a/ChangeLog.md b/ChangeLog.md
@@ -2,6 +2,10 @@
 
 ## [Unreleased]
 
+## [0.1.4.2] - 2021-10-14
+### Changed
+- More types of multiline properties are supported.
+
 ## [0.1.4.1] - 2021-10-07
 ### Changed
 - CI fix

diff --git a/package.yaml b/package.yaml
@@ -1,5 +1,5 @@
 name:                cobot-io
-version:             0.1.4.1
+version:             0.1.4.2
 github:              "biocad/cobot-io"
 license:             BSD3
 category:            Bio

diff --git a/src/Bio/GB/Parser.hs b/src/Bio/GB/Parser.hs
@@ -5,17 +5,20 @@ module Bio.GB.Parser
   , rangeP
   ) where
 
-import Bio.GB.Type                (Feature (..), Form (..), GenBankSequence (..), Locus (..),
-                                   Meta (..), Parser, Reference (..), Source (..), Version (..))
-import Bio.Sequence               (Border (..), MarkedSequence, Range (..), RangeBorder (..),
-                                   markedSequence, shiftRange)
-import Control.Monad.Combinators  (many, manyTill, optional, some, (<|>))
-import Data.Char                  (isAlphaNum, isSpace, isUpper)
-import Data.Functor               (($>))
-import Data.Text                  (Text, intercalate, pack, splitOn, unpack)
-import Text.Megaparsec            (option, satisfy, sepBy1, takeWhile1P, takeWhileP, try, (<?>))
-import Text.Megaparsec.Char       (char, digitChar, eol, letterChar, string)
-import Text.Megaparsec.Char.Lexer (decimal)
+import           Bio.GB.Type                (Feature (..), Form (..), GenBankSequence (..),
+                                             Locus (..), Meta (..), Parser, Reference (..),
+                                             Source (..), Version (..))
+import           Bio.Sequence               (Border (..), MarkedSequence, Range (..),
+                                             RangeBorder (..), markedSequence, shiftRange)
+import           Control.Monad.Combinators  (many, manyTill, optional, some, (<|>))
+import           Data.Char                  (isAlphaNum, isSpace, isUpper)
+import           Data.Functor               (($>))
+import           Data.Text                  (Text, intercalate, pack, splitOn, unpack)
+import qualified Data.Text                  as T
+import           Text.Megaparsec            (notFollowedBy, option, satisfy, sepBy1, takeWhile1P,
+                                             takeWhileP, try, (<?>))
+import           Text.Megaparsec.Char       (char, digitChar, eol, letterChar, string)
+import           Text.Megaparsec.Char.Lexer (decimal)
 
 -- | Parser of .gb file.
 --
@@ -164,13 +167,28 @@ propsP = do
     propName <- takeWhile1P Nothing (/= '=')
     _ <- char '='
 
-    propText <- try ((char '\"' *> takeWhile1P Nothing (/= '\"') <* char '\"')
-             <|> textWithSpacesP)
-             <* eolSpaceP
+    propText <- try ((char '\"' *> takeWhile1P Nothing (/= '\"') <* char '\"' <* eolSpaceP)
+             <|> multiLineProp)
 
     let propTextCorrect = mconcat $ filter (/= featureIndent2) $ splitOn featureIndent2 propText
 
     pure (propName, propTextCorrect)
+  where
+    indLine :: Parser Text
+    indLine = do
+        _ <- string featureIndent2
+        notFollowedBy (char '/')
+        text <- textWithSpacesP 
+        eolSpaceP
+        pure text
+
+    multiLineProp :: Parser Text
+    multiLineProp = do
+        fstText <- textWithSpacesP <* eolSpaceP 
+        rest <- many (try indLine)
+        pure $ T.concat (fstText : rest) 
+
+
 
 -- | First level of identation in FEATURES table file.
 --

diff --git a/test/GB/fromYanaWithLove.gb b/test/GB/fromYanaWithLove.gb
@@ -17,6 +17,7 @@ FEATURES             Location/Qualifiers
                      /mol_type="other DNA"
      rep_origin      join(1,6551..6951)
                      /label=pUCorigin
+                      and also a multiline property
                      /note="/vntifkey=33"
      enhancer        449..858
                      /label=cmv enhanser

diff --git a/test/GBParserSpec.hs b/test/GBParserSpec.hs
@@ -226,7 +226,7 @@ sophisticatedFeatures =
     , preciseSpan (0, 6950))
 
   , (Feature "rep_origin" 
-      [ ("label", "pUCorigin")
+      [ ("label", "pUCorigin and also a multiline property")
       , ("note", "/vntifkey=33")
       ]
     , Join [Point 0, preciseSpan (6550, 6950)])