version 0.1.2.5: fix FASTA-parser for the spaces (#24)

* version 0.1.2.5: fix FASTA-parser for the spaces * added empty test
biocad · Dec 25, 2019 · 4af28a8 · 4af28a8
1 parent 3c5e1c4
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diff --git a/ChangeLog.md b/ChangeLog.md
@@ -2,6 +2,10 @@
 
 ## [Unreleased]
 
+## [0.1.2.5] - 2019-12-24
+### Fixed
+- Possibility to have spaces in Fasta sequences.
+
 ## [0.1.2.4] - 2019-12-23
 ### Added
 - Preprocessing for pdb-files.

diff --git a/package.yaml b/package.yaml
@@ -1,5 +1,5 @@
 name:                cobot-io
-version:             0.1.2.4
+version:             0.1.2.5
 github:              "less-wrong/cobot-io"
 license:             BSD3
 category:            Bio 

diff --git a/src/Bio/FASTA/Parser.hs b/src/Bio/FASTA/Parser.hs
@@ -2,12 +2,13 @@ module Bio.FASTA.Parser
   ( fastaP
   ) where
 
-import           Bio.FASTA.Type         (Fasta, FastaItem(..))
-import           Bio.Sequence           (BareSequence, bareSequence)
-import           Data.Attoparsec.Text   (Parser, many', many1', char, endOfLine, letter,
-                                            takeWhile, choice, endOfInput)
-import           Data.Text              (Text, strip)
-import           Prelude         hiding (takeWhile)
+import           Bio.FASTA.Type       (Fasta, FastaItem (..))
+import           Bio.Sequence         (BareSequence, bareSequence)
+import           Data.Attoparsec.Text (Parser, char, choice, endOfInput,
+                                       endOfLine, letter, many', many1',
+                                       takeWhile)
+import           Data.Text            (Text, strip)
+import           Prelude              hiding (takeWhile)
 
 -- | Parser of .fasta file.
 --
@@ -23,8 +24,8 @@ seqName = strip <$> (char '>' *> tabs *> takeWhile (`notElem` ['\n', '\r']) <* t
 fastaSeq :: Parser (BareSequence Char)
 fastaSeq = bareSequence . mconcat <$> many' line
 
-line :: Parser (String)
-line = many1' letter <* eol
+line :: Parser String
+line = concat <$> many1' (many1' letter <* many' (char ' ')) <* eol
 
 eol :: Parser ()
 eol = tabs *> choice [slashN, endOfInput]

diff --git a/src/Bio/FASTA/Type.hs b/src/Bio/FASTA/Type.hs
@@ -7,7 +7,8 @@ import           Bio.Sequence (BareSequence)
 import           Data.Text    (Text)
 
 -- | Type alias for FASTA file.
---  satisfies the following format : >(\s|\t)*[^\n\r]+(\s|\t)*(\n|\r)*(\w(\n|\r)*)*
+--  satisfies the following format : >(\s|\t)*[^\n\r]+(\s|\t)*(\n|\r)*((\w|\s)(\n|\r)*)*
+--
 type Fasta a = [FastaItem a]
 
 -- | One record in FASTA file.

diff --git a/test/FASTA/correct.fasta b/test/FASTA/correct.fasta
@@ -4,4 +4,14 @@ VLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL
 
 >7HMX:A|PDBID|CHAIN|SEQUENCE
 EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
-VLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL
+VLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL
+
+> With_spaces 
+MDFFDLDIEI KQERLPAECS LNSPLNYSLS AQLTDRMTPR TENVRRQRER
+MDFFDLDIEI KQERLPAECS LNSPLNYSLS AQLTDRMTPR TENVRRQRER
+
+MDFFDLDIEI KQERLPAECS LNSPLNYSLS AQLTDRMTPR TENVRRQRER
+
+> Empty_ha_ha_ha 
+
+
diff --git a/test/FASTASpec.hs b/test/FASTASpec.hs
@@ -10,7 +10,11 @@ import           System.Directory (removeFile)
 import           Test.Hspec
 
 correctFasta :: Fasta Char
-correctFasta = [FastaItem "3HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL"), FastaItem "7HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL")]
+correctFasta = [ FastaItem "3HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL")
+               , FastaItem "7HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL")
+               , FastaItem "With_spaces" (bareSequence "MDFFDLDIEIKQERLPAECSLNSPLNYSLSAQLTDRMTPRTENVRRQRERMDFFDLDIEIKQERLPAECSLNSPLNYSLSAQLTDRMTPRTENVRRQRERMDFFDLDIEIKQERLPAECSLNSPLNYSLSAQLTDRMTPRTENVRRQRER")
+               , FastaItem "Empty_ha_ha_ha" (bareSequence "")
+               ]
 
 fastaSpec :: Spec
 fastaSpec = describe "Fasta file parser." $ do