From 061e1d4310cd0ff3e1efacd5a6898d6dccf11a3f Mon Sep 17 00:00:00 2001
From: Maxim Koltsov <kolmax94@gmail.com>
Date: Tue, 4 Oct 2022 10:54:34 +0300
Subject: [PATCH] version 0.1.5.0 rewrite FASTA parser to Megaparsec (#67)
Co-authored-by: Grigoriy <mikheevg@Grigoriys-MacBook-Pro.local>
Co-authored-by: Grigoriy Mikheev <grigoriymihtt@gmail.com>
Co-authored-by: Grigoriy Mikheev <mikheevg.@biocad.ru>
---
ChangeLog.md | 4 +
default.nix | 12 ++
package.yaml | 3 +-
shell.nix | 1 +
src/Bio/FASTA.hs | 7 +-
src/Bio/FASTA/Parser.hs | 259 +++++++++++++++++++++-------------------
src/Bio/FASTA/Type.hs | 12 +-
test/FASTA/order1.fasta | 14 +++
test/FASTA/order2.fasta | 5 +
test/FASTA/order3.fasta | 2 +
test/FASTA/order4.fasta | 27 +++++
test/FASTA/order5.fasta | 9 ++
test/FASTA/order6.fasta | 26 ++++
test/FASTA/order7.fasta | 11 ++
test/FASTA/order8.fasta | 22 ++++
test/FASTASpec.hs | 86 +++++++++----
test/FastaParserSpec.hs | 70 +++++++----
17 files changed, 394 insertions(+), 176 deletions(-)
create mode 100644 default.nix
create mode 100644 shell.nix
create mode 100644 test/FASTA/order1.fasta
create mode 100644 test/FASTA/order2.fasta
create mode 100644 test/FASTA/order3.fasta
create mode 100644 test/FASTA/order4.fasta
create mode 100644 test/FASTA/order5.fasta
create mode 100644 test/FASTA/order6.fasta
create mode 100644 test/FASTA/order7.fasta
create mode 100644 test/FASTA/order8.fasta
diff --git a/ChangeLog.md b/ChangeLog.md
index 841c1a7..3cec239 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -2,6 +2,10 @@
## [Unreleased]
+## [0.1.5.0] - 2022-09-30
+### Changed
+- Update FASTA parser to megaparsec.
+
## [0.1.4.4] - 2022-06-02
### Changed
- Update more dependencies;
diff --git a/default.nix b/default.nix
new file mode 100644
index 0000000..314ae3b
--- /dev/null
+++ b/default.nix
@@ -0,0 +1,12 @@
+let
+ bcd-lts = import (builtins.fetchGit {
+ url = "git@github.com:biocad/nix-lts.git";
+ ref = "master";
+ });
+in
+bcd-lts.mkBiocadProject {
+ src = bcd-lts.pkgs.haskell-nix.haskellLib.cleanGit { name = "cobot-io"; src = ./.; };
+ shellArgs = {
+ buildInputs = [ bcd-lts.pkgs.RNA ];
+ };
+}
diff --git a/package.yaml b/package.yaml
index 0d4cde8..21dd9d0 100644
--- a/package.yaml
+++ b/package.yaml
@@ -1,5 +1,5 @@
name: cobot-io
-version: 0.1.4.4
+version: 0.1.5.0
github: "biocad/cobot-io"
license: BSD3
category: Bio
@@ -41,6 +41,7 @@ dependencies:
- containers >= 0.5.7.1 && < 0.7
- data-msgpack >= 0.0.9 && < 0.1
- deepseq >= 1.4 && < 1.5
+- filepath
- http-conduit >= 2.3 && < 2.4
- hyraxAbif >= 0.2.3.27 && < 0.2.4.0
- lens >= 4.16 && < 5.2
diff --git a/shell.nix b/shell.nix
new file mode 100644
index 0000000..76918f6
--- /dev/null
+++ b/shell.nix
@@ -0,0 +1 @@
+(import ./default.nix).shellFor
diff --git a/src/Bio/FASTA.hs b/src/Bio/FASTA.hs
index d9dfbba..0c2ff4b 100644
--- a/src/Bio/FASTA.hs
+++ b/src/Bio/FASTA.hs
@@ -6,14 +6,15 @@ module Bio.FASTA
, fromFile
, toFile
, fastaP
- , fastaPGeneric
, fastaLine
, modificationP
+ , Parser
) where
import Control.Monad.IO.Class (MonadIO, liftIO)
-import Data.Attoparsec.Text (parseOnly)
import Data.Text.IO (readFile, writeFile)
+import System.FilePath (takeBaseName)
+import Text.Megaparsec (errorBundlePretty, parse)
#if !MIN_VERSION_base(4,13,0)
import Control.Monad.Fail (MonadFail (..))
import Prelude hiding (fail, readFile, writeFile)
@@ -28,7 +29,7 @@ import Bio.FASTA.Writer (WritableFastaToken (..), fastaToText)
-- | Reads 'FastaSequence' from given file.
--
fromFile :: (MonadFail m, MonadIO m) => FilePath -> m (Fasta Char)
-fromFile f = liftIO (readFile f) >>= either fail pure . parseOnly fastaP
+fromFile f = liftIO (readFile f) >>= either (fail . errorBundlePretty) pure . parse fastaP (takeBaseName f)
-- | Writes 'FastaSequence' to file.
--
diff --git a/src/Bio/FASTA/Parser.hs b/src/Bio/FASTA/Parser.hs
index a5aa3a1..4eb7cc0 100644
--- a/src/Bio/FASTA/Parser.hs
+++ b/src/Bio/FASTA/Parser.hs
@@ -2,151 +2,168 @@
module Bio.FASTA.Parser
( fastaP
- , fastaPGeneric
- , fastaLine
+ , fastaLine
+ , parseOnly
, modificationP
+ , fastaPGeneric
+ , Parser
) where
-import Bio.FASTA.Type (Fasta, FastaItem (..), ModItem (..), Modification (..),
- ParsableFastaToken (..))
-import Bio.Sequence (BareSequence, bareSequence)
-import Control.Applicative ((<|>))
-import Data.Attoparsec.Text (Parser, char, choice, endOfInput, endOfLine, many', many1', satisfy,
- skipWhile, space, string, takeWhile, try)
-import Data.Char (isAlphaNum, isLetter, isSpace)
-import Data.Text (Text, strip)
-import Prelude hiding (takeWhile)
+import Bio.FASTA.Type (Fasta, FastaItem (..),
+ ModItem (..), Modification (..),
+ ParsableFastaToken (..))
+import Bio.Sequence (BareSequence, bareSequence)
+import Data.Bifunctor (first)
+import Data.Char (isLetter)
+import Data.Functor (void, ($>))
+import Data.Text (Text, pack, strip)
+import Data.Void (Void)
+import Text.Megaparsec
+import Text.Megaparsec.Char
+import qualified Text.Megaparsec.Char.Lexer as L
instance ParsableFastaToken Char where
- parseToken = satisfy
+ parseToken p = satisfy p <?> "letter"
instance ParsableFastaToken ModItem where
- parseToken predicate = (Mod <$> modificationP) <|> (Letter <$> satisfy predicate)
+ parseToken p = (Mod <$> modificationP <?> "fasta item modification") <|> (Letter <$> satisfy p <?> "letter")
+type Parser = Parsec Void Text
-- | Parser of .fasta file.
--
+
+parseOnly :: Parsec Void Text a -> Text -> Either String a
+parseOnly p s = first errorBundlePretty $ parse p "input.fasta" s
+
+sc :: Parser ()
+sc = L.space space1 empty empty
+
+lexeme :: Parser a -> Parser a
+lexeme = L.lexeme sc
+
+symbol :: Text -> Parser Text
+symbol = L.symbol sc
+
fastaP :: ParsableFastaToken a => Parser (Fasta a)
-fastaP = many' space *> fastaPGeneric isLetter
+fastaP = many (item isLetter) <* hidden space <* eof
fastaPGeneric :: ParsableFastaToken a => (Char -> Bool) -> Parser (Fasta a)
-fastaPGeneric = many' . item
+fastaPGeneric p = many (item p) <* hidden space <* eof
item :: ParsableFastaToken a => (Char -> Bool) -> Parser (FastaItem a)
-item predicate = (FastaItem <$> seqName <*> fastaSeq predicate) <* skipWhile isSpace
+item p =
+ FastaItem
+ <$> seqName
+ <*> (fastaSeq p <?> "sequence")
seqName :: Parser Text
-seqName = strip <$> (char '>' *> tabs *> takeWhile (`notElem` ['\n', '\r']) <* tabs <* eol)
+seqName = strip . pack <$> (symbol ">" *> (manyTill anySingle myEnd <?> "sequence name"))
fastaSeq :: ParsableFastaToken a => (Char -> Bool) -> Parser (BareSequence a)
-fastaSeq predicate = bareSequence . mconcat <$> many' (fastaLine predicate)
+fastaSeq p = bareSequence . concat <$> many (fastaLine p) <* hidden space
fastaLine :: ParsableFastaToken a => (Char -> Bool) -> Parser [a]
-fastaLine predicate = concat <$> many1' (many1' (parseToken predicate) <* many' (char ' ')) <* eol
-
-eol :: Parser ()
-eol = tabs *> choice [slashN, endOfInput]
-
-slashN :: Parser ()
-slashN = () <$ many1' endOfLine
+fastaLine p = concat <$> some (some (parseToken p) <* hidden hspace) <* myEnd
-tabs :: Parser ()
-tabs = () <$ many' (char '\t')
+myEnd :: Parser ()
+myEnd = void (some eol) <|> eof
modificationP :: Parser Modification
-modificationP
- = string "[A*]" *> pure Mod_A_Star
- <|> string "[C*]" *> pure Mod_C_Star
- <|> string "[G*]" *> pure Mod_G_Star
- <|> string "[T*]" *> pure Mod_T_Star
- <|> string "[rA]" *> pure Mod_rA
- <|> string "[rC]" *> pure Mod_rC
- <|> string "[rG]" *> pure Mod_rG
- <|> string "[rU]" *> pure Mod_rU
- <|> string "[+A]" *> pure Mod_Plus_A
- <|> string "[+C]" *> pure Mod_Plus_C
- <|> string "[+G]" *> pure Mod_Plus_G
- <|> string "[+T]" *> pure Mod_Plus_T
- <|> string "[rAf]" *> pure Mod_rAf
- <|> string "[rCf]" *> pure Mod_rCf
- <|> string "[rGf]" *> pure Mod_rGf
- <|> string "[rUf]" *> pure Mod_rUf
- <|> string "[mA]" *> pure Mod_mA
- <|> string "[mC]" *> pure Mod_mC
- <|> string "[mG]" *> pure Mod_mG
- <|> string "[mU]" *> pure Mod_mU
- <|> string "[mA*]" *> pure Mod_mA_Star
- <|> string "[mC*]" *> pure Mod_mC_Star
- <|> string "[mG*]" *> pure Mod_mG_Star
- <|> string "[mU*]" *> pure Mod_mU_Star
- <|> string "[dU]" *> pure Mod_dU
- <|> string "[5Bio]" *> pure Mod_5Bio
- <|> string "[iBio]" *> pure Mod_iBio
- <|> string "[56FAM]" *> pure Mod_56FAM
- <|> string "[36FAM]" *> pure Mod_36FAM
- <|> string "[5HEX]" *> pure Mod_5HEX
- <|> string "[5TMR]" *> pure Mod_5TMR
- <|> string "[3BHQ1]" *> pure Mod_3BHQ1
- <|> string "[3BHQ2]" *> pure Mod_3BHQ2
- <|> string "[5NH2]" *> pure Mod_5NH2
- <|> string "[3NH2]" *> pure Mod_3NH2
- <|> string "[5PO4]" *> pure Mod_5PO4
- <|> string "[3PO4]" *> pure Mod_3PO4
- <|> string "[3BioTEG]" *> pure Mod_3BioTEG
- <|> string "[C12]" *> pure Mod_C12
- <|> string "[NHSdT]" *> pure Mod_NHSdT
- <|> string "[5Mal]" *> pure Mod_5Mal
- <|> string "[5thio]" *> pure Mod_5thio
- <|> string "[3thio]" *> pure Mod_3thio
- <|> string "[3azide]" *> pure Mod_3azide
- <|> string "[3alkine]" *> pure Mod_3alkine
- <|> string "[5CholTEG]" *> pure Mod_5CholTEG
- <|> string "[3CholTEG]" *> pure Mod_3CholTEG
- <|> string "[5C10]" *> pure Mod_5C10
- <|> string "[5Alk]" *> pure Mod_5Alk
- <|> string "[GC]" *> pure Mod_GC
- <|> string "[GT]" *> pure Mod_GT
- <|> string "[AT]" *> pure Mod_AT
- <|> string "[TG]" *> pure Mod_TG
- <|> string "[AC]" *> pure Mod_AC
- <|> string "[CC]" *> pure Mod_CC
- <|> string "[AA]" *> pure Mod_AA
- <|> string "[TC]" *> pure Mod_TC
- <|> string "[TT]" *> pure Mod_TT
- <|> string "[CG]" *> pure Mod_CG
- <|> string "[GG]" *> pure Mod_GG
- <|> string "[AG]" *> pure Mod_AG
- <|> string "[GA]" *> pure Mod_GA
- <|> string "[CA]" *> pure Mod_CA
- <|> string "[CT]" *> pure Mod_CT
- <|> string "[TA]" *> pure Mod_TA
- <|> string "[AAA]" *> pure Mod_AAA
- <|> string "[AAC]" *> pure Mod_AAC
- <|> string "[ACT]" *> pure Mod_ACT
- <|> string "[ATC]" *> pure Mod_ATC
- <|> string "[ATG]" *> pure Mod_ATG
- <|> string "[CAG]" *> pure Mod_CAG
- <|> string "[AGA]" *> pure Mod_AGA
- <|> string "[CAT]" *> pure Mod_CAT
- <|> string "[CCG]" *> pure Mod_CCG
- <|> string "[CGT]" *> pure Mod_CGT
- <|> string "[CTG]" *> pure Mod_CTG
- <|> string "[GAA]" *> pure Mod_GAA
- <|> string "[GAC]" *> pure Mod_GAC
- <|> string "[GCT]" *> pure Mod_GCT
- <|> string "[GGT]" *> pure Mod_GGT
- <|> string "[GTT]" *> pure Mod_GTT
- <|> string "[TAC]" *> pure Mod_TAC
- <|> string "[TCT]" *> pure Mod_TCT
- <|> string "[TGC]" *> pure Mod_TGC
- <|> string "[TGG]" *> pure Mod_TGG
- <|> string "[TTC]" *> pure Mod_TTC
- <|> string "[TTT]" *> pure Mod_TTT
- <|> unknownP
+modificationP
+ = choice
+ [ string "[A*]" $> Mod_A_Star
+ , string "[C*]" $> Mod_C_Star
+ , string "[G*]" $> Mod_G_Star
+ , string "[T*]" $> Mod_T_Star
+ , string "[rA]" $> Mod_rA
+ , string "[rC]" $> Mod_rC
+ , string "[rG]" $> Mod_rG
+ , string "[rU]" $> Mod_rU
+ , string "[+A]" $> Mod_Plus_A
+ , string "[+C]" $> Mod_Plus_C
+ , string "[+G]" $> Mod_Plus_G
+ , string "[+T]" $> Mod_Plus_T
+ , string "[rAf]" $> Mod_rAf
+ , string "[rCf]" $> Mod_rCf
+ , string "[rGf]" $> Mod_rGf
+ , string "[rUf]" $> Mod_rUf
+ , string "[mA]" $> Mod_mA
+ , string "[mC]" $> Mod_mC
+ , string "[mG]" $> Mod_mG
+ , string "[mU]" $> Mod_mU
+ , string "[mA*]" $> Mod_mA_Star
+ , string "[mC*]" $> Mod_mC_Star
+ , string "[mG*]" $> Mod_mG_Star
+ , string "[mU*]" $> Mod_mU_Star
+ , string "[dU]" $> Mod_dU
+ , string "[5Bio]" $> Mod_5Bio
+ , string "[iBio]" $> Mod_iBio
+ , string "[56FAM]" $> Mod_56FAM
+ , string "[36FAM]" $> Mod_36FAM
+ , string "[5HEX]" $> Mod_5HEX
+ , string "[5TMR]" $> Mod_5TMR
+ , string "[3BHQ1]" $> Mod_3BHQ1
+ , string "[3BHQ2]" $> Mod_3BHQ2
+ , string "[5NH2]" $> Mod_5NH2
+ , string "[3NH2]" $> Mod_3NH2
+ , string "[5PO4]" $> Mod_5PO4
+ , string "[3PO4]" $> Mod_3PO4
+ , string "[3BioTEG]" $> Mod_3BioTEG
+ , string "[C12]" $> Mod_C12
+ , string "[NHSdT]" $> Mod_NHSdT
+ , string "[5Mal]" $> Mod_5Mal
+ , string "[5thio]" $> Mod_5thio
+ , string "[3thio]" $> Mod_3thio
+ , string "[3azide]" $> Mod_3azide
+ , string "[3alkine]" $> Mod_3alkine
+ , string "[5CholTEG]" $> Mod_5CholTEG
+ , string "[3CholTEG]" $> Mod_3CholTEG
+ , string "[5C10]" $> Mod_5C10
+ , string "[5Alk]" $> Mod_5Alk
+ , string "[GC]" $> Mod_GC
+ , string "[GT]" $> Mod_GT
+ , string "[AT]" $> Mod_AT
+ , string "[TG]" $> Mod_TG
+ , string "[AC]" $> Mod_AC
+ , string "[CC]" $> Mod_CC
+ , string "[AA]" $> Mod_AA
+ , string "[TC]" $> Mod_TC
+ , string "[TT]" $> Mod_TT
+ , string "[CG]" $> Mod_CG
+ , string "[GG]" $> Mod_GG
+ , string "[AG]" $> Mod_AG
+ , string "[GA]" $> Mod_GA
+ , string "[CA]" $> Mod_CA
+ , string "[CT]" $> Mod_CT
+ , string "[TA]" $> Mod_TA
+ , string "[AAA]" $> Mod_AAA
+ , string "[AAC]" $> Mod_AAC
+ , string "[ACT]" $> Mod_ACT
+ , string "[ATC]" $> Mod_ATC
+ , string "[ATG]" $> Mod_ATG
+ , string "[CAG]" $> Mod_CAG
+ , string "[AGA]" $> Mod_AGA
+ , string "[CAT]" $> Mod_CAT
+ , string "[CCG]" $> Mod_CCG
+ , string "[CGT]" $> Mod_CGT
+ , string "[CTG]" $> Mod_CTG
+ , string "[GAA]" $> Mod_GAA
+ , string "[GAC]" $> Mod_GAC
+ , string "[GCT]" $> Mod_GCT
+ , string "[GGT]" $> Mod_GGT
+ , string "[GTT]" $> Mod_GTT
+ , string "[TAC]" $> Mod_TAC
+ , string "[TCT]" $> Mod_TCT
+ , string "[TGC]" $> Mod_TGC
+ , string "[TGG]" $> Mod_TGG
+ , string "[TTC]" $> Mod_TTC
+ , string "[TTT]" $> Mod_TTT
+ , unknownP
+ ]
unknownP :: Parser Modification
-unknownP = try $ do
- _ <- char '['
- m <- many1' $ satisfy (\c -> isAlphaNum c || c `elem` ['+', '-', '*', '_'])
- _ <- char ']'
- pure $ Unknown ("[" <> m <> "]")
+unknownP = do
+ res <- between (symbol "[") (symbol "]")
+ (lexeme (some (alphaNumChar <|> choice (char <$> ['+', '-', '*', '_'])) <?> "modification name"))
+ pure $ Unknown ("[" <> res <> "]")
diff --git a/src/Bio/FASTA/Type.hs b/src/Bio/FASTA/Type.hs
index bb5a86f..f599e5c 100644
--- a/src/Bio/FASTA/Type.hs
+++ b/src/Bio/FASTA/Type.hs
@@ -7,10 +7,11 @@ module Bio.FASTA.Type
, modificationToString
) where
-import Bio.Sequence (BareSequence)
-import Data.Attoparsec.Text (Parser)
-import Data.Text (Text)
-import GHC.Generics (Generic)
+import Bio.Sequence (BareSequence)
+import Data.Text (Text)
+import Data.Void
+import GHC.Generics (Generic)
+import Text.Megaparsec
-- | Type alias for FASTA file.
-- satisfies the following format : >(\s|\t)*[^\n\r]+(\s|\t)*(\n|\r)*((\w|\s)(\n|\r)*)*
@@ -29,7 +30,7 @@ data FastaItem a
deriving (Eq, Show, Functor)
class ParsableFastaToken a where
- parseToken :: (Char -> Bool) -> Parser a
+ parseToken :: (Char -> Bool) -> Parsec Void Text a
data ModItem
= Mod Modification
@@ -216,4 +217,3 @@ modificationToString Mod_TGG = "[TGG]"
modificationToString Mod_TTC = "[TTC]"
modificationToString Mod_TTT = "[TTT]"
modificationToString (Unknown s) = s
-
diff --git a/test/FASTA/order1.fasta b/test/FASTA/order1.fasta
new file mode 100644
index 0000000..927b811
--- /dev/null
+++ b/test/FASTA/order1.fasta
@@ -0,0 +1,14 @@
+>3HMX:A|PDBID|CHAIN|SEQUENCE
+IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSE
+VLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL
+
+>7HMX:A|PDBID|CHAIN|SEQUENCE
+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
+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/FASTA/order2.fasta b/test/FASTA/order2.fasta
new file mode 100644
index 0000000..3f70512
--- /dev/null
+++ b/test/FASTA/order2.fasta
@@ -0,0 +1,5 @@
+>Sample_name1
+ACGT....TCG
+
+>Sample_name2
+GTCA....TGC
\ No newline at end of file
diff --git a/test/FASTA/order3.fasta b/test/FASTA/order3.fasta
new file mode 100644
index 0000000..e690170
--- /dev/null
+++ b/test/FASTA/order3.fasta
@@ -0,0 +1,2 @@
+>N-His-E4Orf6-7-R2(115)
+TGATGGTGATGGTGATGcatGTGGTAAACTCGACTTTCACTTTTCTCTATCACTGATAGGGAGTGGTAAACTCGACTTTCACTTTTCTCTATCACTGATAGGGAaacagtcagcc
\ No newline at end of file
diff --git a/test/FASTA/order4.fasta b/test/FASTA/order4.fasta
new file mode 100644
index 0000000..38de7ad
--- /dev/null
+++ b/test/FASTA/order4.fasta
@@ -0,0 +1,27 @@
+>CMV-Lox2272-HindIII_R
+aatcatAAGCTTataacttcgtataaagtatcctatacgaagttatagctctgcttatatagacctcccacc
+
+
+HindIII-BFP_F
+aagttatAAGCTTatgagcgagctgattaaggagaacatgc
+
+>sPA-lox2272_R
+taatTGGCTAGCATataacttcgtataaagtatcctatacgaagttatgctgcatcacacaaaaaaccaacac
+
+>NheI-GFP_F
+ttatATGCTAGCCAatggtgagcaagggcgagg
+
+>NotI-pMP_F
+tataatGCGGCCGCAGGTGGCac
+
+>CMV-LoxP-HindIII_R
+attaatAAGCTTataacttcgtataatgtatgctatacgaagttatagctctgcttatatagacctcccacc
+
+>sPA-NotI_R
+aattaaTGCGGCCGCgctgcatcacacaaaaaaccaacacac
+
+sPA-LoxP-NheI_R
+taatTGGCTAGCATataacttcgtataatgtatgctatacgaagttatgctgcatcacacaaaaaaccaacac
+
+
+
\ No newline at end of file
diff --git a/test/FASTA/order5.fasta b/test/FASTA/order5.fasta
new file mode 100644
index 0000000..5979123
--- /dev/null
+++ b/test/FASTA/order5.fasta
@@ -0,0 +1,9 @@
+>qCHO49 F
+TGGAGAGATGGCTCGAGGTT
+
+
+
+
+
+qCHO R
+TGGTTGCTGGGAATTGAACTC
diff --git a/test/FASTA/order6.fasta b/test/FASTA/order6.fasta
new file mode 100644
index 0000000..156488b
--- /dev/null
+++ b/test/FASTA/order6.fasta
@@ -0,0 +1,26 @@
+>CMV-Lox2272-HindIII_R
+aatcatAAGCTTataacttcgtataaagtatcctatacgaagttatagctctgcttatatagacctcccacc
+
+>HindIII-BFP_F
+aagttatAAGCTTatgagcgagctgattaaggagaacatgc
+
+>sPA-lox2272_R
+taatTGGCTAGCATataacttcgtataaagtatcctatacgaagttatgctgcatcacacaaaaaaccaacac
+
+>NheI-GFP_F
+ttatATGCTAGCCAatggtgagcaagggcgagg
+
+>NotI-pMP_F
+tataatGCGGCCGCAGGTGGCac
+
+>CMV-LoxP-HindIII_R
+attaatAAGCTTataacttcgtataatgtatgctatacgaagttatagctctgcttatatagacctcccacc
+
+>sPA-NotI_R
+aattaaTGCGGCCGCgctgcatcacacaaaaaaccaacacac
+
+sPA-LoxP-NheI_R
+taatTGGCTAGCATataacttcgtataatgtatgctatacgaagttatgctgcatcacacaaaaaaccaacac
+
+
+
\ No newline at end of file
diff --git a/test/FASTA/order7.fasta b/test/FASTA/order7.fasta
new file mode 100644
index 0000000..0a097f5
--- /dev/null
+++ b/test/FASTA/order7.fasta
@@ -0,0 +1,11 @@
+>GB_F
+5’-CTTCAAGAGAGAGACCTGCGT-3’
+
+>GB_R
+5’-GATGTTGTTGGCCACCTCG-3’
+
+>F8_GB20_F
+GCTACACCTTCAAGCACA
+
+>F8_GB20_R
+GGGTTCTCCATGCTCA
diff --git a/test/FASTA/order8.fasta b/test/FASTA/order8.fasta
new file mode 100644
index 0000000..f0fe91c
--- /dev/null
+++ b/test/FASTA/order8.fasta
@@ -0,0 +1,22 @@
+>Ampl_prcTnT_del
+tttttACGCGTtaatagtaatcaattacggggtcattagttcatagcccatatatggagttccggctgccttatcagcgtctcgggcactcacgtatctccgtccgacgggtttaaaatagcaaaactctgagcgctgctgccaaaatagcagctcacaagtgttgcattcctctctgggcgccgggcacattcctgctggctctgcccgccccccatatatggagttccgcgttacataacttacggtaaatgg
+>Ampl_MHCK7-1
+tttttACGCGTtaatagtaatcaattacggggtcattagttcatagcccatatatggagttccgccttcagattaaaaataactgaggtaagggcctgggtaggggaggtggtgtgagacgctcctgtctctcctctatctgcccatcggccctttggggaggaggaatgtgcccaaggactaaaaaaaggccatggagccagaggggcgagggcaacagacctttcatgggcaaaccttggggccctgctgtctagcatgcccc
+>Ampl_MHCK7-2
+accttggggccctgctgtctagcatgccccactacgggtctaggctgcccatgtaaggaggcaaggcctggggacacccgagatgcctggttataattaacccagacatgtggctgcccccccccccccaacacctgctgcctctaaaaataaccctgtccctggtggatcccctgcatgcgaagatcttcgaaccatatatggagttccgcgttacataacttacggtaaatgg
+>Amplicon1_MH
+tttttACGCGTtaatagtaatcaattacggggtcattagttcatagcccatatatggagttccgGTGCTGTCAGCCTTCCTTGACACCTCTGTCTCCTCAGGTGCCTGGCTCCCAGTCCCCAGAACGCCTCTCCTGTACCTTGCTTCCTAGCTGGGCCTTTCCTTCTCCTCTATAAATACCAGCTCTGGTATTTCGCCTTGGCAGCTGTagcagccactacgggtctaggctgcccatgtaaggaggcaaggcctgggga
+>Amplicon2_MH
+gctgcccatgtaaggaggcaaggcctggggacacccgagatgcctggttataattaacccagacatgtggctgcccccccccccccaacacctgctgcctgagcctcacccccaccccggtgcctgggtcttaggctctgtacaccatggaggagaagctcgctctaaaaataaccctgtcccccatatatggagttccgcgttacataacttacggtaaatgg
+>Ampl_MHCK7-1
+tttttACGCGTtaatagtaatcaattacggggtcattagttcatagcccatatatggagttccgccttcagattaaaaataactgaggtaagggcctgggtaggggaggtggtgtgagacgctcctgtctctcctctatctgcccatcggccctttggggaggaggaatgtgcccaaggactaaaaaaaggccatggagccagaggggcgagggcaacagacctttcatgggcaaaccttggggccctgctgtctagcatgcccc
+>Ampl_MHCK7-2
+accttggggccctgctgtctagcatgccccactacgggtctaggctgcccatgtaaggaggcaaggcctggggacacccgagatgcctggttataattaacccagacatgtggctgcccccccccccccaacacctgctgcctctaaaaataaccctgtccctggtggatcccctgcatgcgaagatcttcgaaccatatatggagttccgcgttacataacttacggtaaatgg
+>CMV + enhMH-1
+GTGCTGTCAGCCTTCCTTGACACCTCTGTCTCCTCAGGTGCCTGGCTCCCAGTCCCCAGAACGCCTCTCCTGTACCTTGCTTCCTAGCTGGGCCTTTCCTTCTCCTCTATAAATACCAGCTCTGGTATTTCGCCTTGGCAGCTGTagcagccactacgggtctaggctgcccatgtaaggaggcaaggcctggggacacccgagatgcctggttataattaacccagacatgtggctgcccccccccccccaacacctgctgcctgagcctcacccccaccccggtgcctgggtcttaggctctgtacac
+>CMV + enhMH-2
+cccggtgcctgggtcttaggctctgtacaccatggaggagaagctcgctctaaaaataaccctgtcccgtgatgcggttttggcagtacatcaatgggcgtggatagcggtttgactcacggggatttccaagtctccaccccattgacgtcaatgggagtttgttttggcaccaaaatcaacgggactttccaaaatgtcgtaacaactccgccccattgacgcaaatgggcggtaggcgtgtacggtgggaggtctatataagcagagct
+>CMV + enhMCK + prcTnT-1
+ccactacgggtctaggctgcccatgtaaggaggcaaggcctggggacacccgagatgcctggttataattaaccccaacacctgctgcccccccccccccaacacctgctgcctgagcctgagcggttaccccaccccggtgcctgggtcttaggctctgtacaccatggaggagaagctcgctctaaaaataaccctgtccctggtgggtgccttatcagcgtccccagccctgggaggtgacagctggctggcttgtgtcagcccctcgggcactcacgtatctccgt
+CMV + enhMCK + prcTnT-2
+tcagcccctcgggcactcacgtatctccgtccgacgggtttaaaatagcaaaactgtgatgcggttttggcagtacatcaatgggcgtggatagcggtttgactcacggggatttccaagtctccaccccattgacgtcaatgggagtttgttttggcaccaaaatcaacgggactttccaaaatgtcgtaacaactccgccccattgacgcaaatgggcggtaggcgtgtacggtgggaggtctatataagcagagct
\ No newline at end of file
diff --git a/test/FASTASpec.hs b/test/FASTASpec.hs
index c4f5b0a..01199ff 100644
--- a/test/FASTASpec.hs
+++ b/test/FASTASpec.hs
@@ -2,37 +2,79 @@
module FASTASpec where
-import Bio.FASTA (fromFile, toFile)
-import Bio.FASTA.Type (Fasta, FastaItem (..))
-import Bio.Sequence (bareSequence)
-import Prelude hiding (readFile, writeFile)
-import System.Directory (removeFile)
+import Bio.FASTA (fastaP, fromFile, toFile)
+import Bio.FASTA.Parser (parseOnly)
+import Bio.FASTA.Type (Fasta, FastaItem (..))
+import Bio.Sequence (bareSequence)
+import Control.Monad.IO.Class (liftIO)
+import Data.Text.IO (readFile)
+import Prelude hiding (readFile, writeFile)
+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")
- , FastaItem "With_spaces" (bareSequence "MDFFDLDIEIKQERLPAECSLNSPLNYSLSAQLTDRMTPRTENVRRQRERMDFFDLDIEIKQERLPAECSLNSPLNYSLSAQLTDRMTPRTENVRRQRERMDFFDLDIEIKQERLPAECSLNSPLNYSLSAQLTDRMTPRTENVRRQRER")
- , FastaItem "Empty_ha_ha_ha" (bareSequence "")
- ]
+correctFasta1 :: Fasta Char
+correctFasta1 = [ 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 "")
+ ]
+
+badFasta2 :: Either String (Fasta Char)
+badFasta2 = Left "input.fasta:2:5:\n |\n2 | ACGT....TCG\r\n | ^^\nunexpected \"..\"\nexpecting end of input, end of line, or letter\n"
+
+
+correctFasta3 :: Fasta Char
+correctFasta3 = [ FastaItem "N-His-E4Orf6-7-R2(115)" (bareSequence "TGATGGTGATGGTGATGcatGTGGTAAACTCGACTTTCACTTTTCTCTATCACTGATAGGGAGTGGTAAACTCGACTTTCACTTTTCTCTATCACTGATAGGGAaacagtcagcc")
+ ]
+
+badFasta4 :: Either String (Fasta Char)
+badFasta4 = Left "input.fasta:5:8:\n |\n5 | HindIII-BFP_F \r\n | ^^\nunexpected \"-B\"\nexpecting end of input, end of line, or letter\n"
+
+correctFasta5 :: Fasta Char
+correctFasta5 = [FastaItem "qCHO49 F" (bareSequence "TGGAGAGATGGCTCGAGGTTqCHORTGGTTGCTGGGAATTGAACTC")]
+
+badFasta6 :: Either String (Fasta Char)
+badFasta6 = Left "input.fasta:22:1:\n |\n22 | sPA-LoxP-NheI_R \r\n | ^\nunexpected 's'\nexpecting '>' or end of input\n"
+
+badFasta7 :: Either String (Fasta Char)
+badFasta7 = Left "input.fasta:2:1:\n |\n2 | 5\8217-CTTCAAGAGAGAGACCTGCGT-3\8217\r\n | ^\nunexpected '5'\nexpecting '>', end of input, end of line, or sequence\n"
+
+badFasta8 :: Either String (Fasta Char)
+badFasta8 = Left "input.fasta:21:5:\n |\n21 | CMV + enhMCK + prcTnT-2\r\n | ^^\nunexpected \"+ \"\nexpecting end of input, end of line, or letter\n"
fastaSpec :: Spec
-fastaSpec = describe "Fasta file parser." $ do
- parseFile "test/FASTA/correct.fasta"
- writeFile "test/FASTA/test.fasta"
+fastaSpec = describe "Fasta files parser." $ do
+ parseFile "test/FASTA/order1.fasta" correctFasta1
+ writeFile "test/FASTA/input.fasta" correctFasta1
+ parseBadFile "test/FASTA/order2.fasta" badFasta2
+ parseFile "test/FASTA/order3.fasta" correctFasta3
+ writeFile "test/FASTA/input.fasta" correctFasta3
+ parseBadFile "test/FASTA/order4.fasta" badFasta4
+ parseFile "test/FASTA/order5.fasta" correctFasta5
+ writeFile "test/FASTA/input.fasta" correctFasta5
+ parseBadFile "test/FASTA/order6.fasta" badFasta6
+ parseBadFile "test/FASTA/order7.fasta" badFasta7
+ parseBadFile "test/FASTA/order8.fasta" badFasta8
-parseFile :: FilePath -> Spec
-parseFile path = do
+parseFile :: FilePath -> Fasta Char -> Spec
+parseFile path cf = do
describe "fromFile" $ do
it "correctly parses fasta from file" $ do
fasta <- fromFile path
- fasta `shouldBe` correctFasta
+ fasta `shouldBe` cf
-writeFile :: FilePath -> Spec
-writeFile path = describe "writeFile" $ do
+parseBadFile :: FilePath -> Either String (Fasta Char) -> Spec
+parseBadFile path cf = do
+ describe "fromFile" $ do
+ it "correctly parses fasta from file" $ do
+ res <- liftIO (readFile path)
+ let badRes = parseOnly fastaP res
+ badRes `shouldBe` cf
+
+writeFile :: FilePath -> Fasta Char -> Spec
+writeFile path cf = describe "writeFile" $ do
it "correctly write fasta into file" $ do
- toFile correctFasta path
+ toFile cf path
fasta <- fromFile path
removeFile path
- fasta `shouldBe` correctFasta
-
+ fasta `shouldBe` cf
diff --git a/test/FastaParserSpec.hs b/test/FastaParserSpec.hs
index 25cda17..5378595 100644
--- a/test/FastaParserSpec.hs
+++ b/test/FastaParserSpec.hs
@@ -1,18 +1,19 @@
{-# LANGUAGE OverloadedStrings #-}
-{-# LANGUAGE TypeApplications #-}
+{-# LANGUAGE TypeApplications #-}
module FastaParserSpec where
-import Bio.FASTA.Parser (fastaP)
-import Bio.FASTA.Type (Fasta, FastaItem (..), ModItem (..), Modification (..))
-import Bio.Sequence (bareSequence)
-import Data.Attoparsec.Text (endOfInput, parseOnly)
-import Data.Text (Text)
-import qualified Data.Text as T
+import Bio.FASTA.Parser (fastaP, parseOnly)
+import Bio.FASTA.Type (Fasta, FastaItem (..), ModItem (..), Modification (..))
+import Bio.Sequence (bareSequence)
+import Data.Bifunctor
+import Data.Text (Text)
+import qualified Data.Text as T
import Test.Hspec
+import Text.Megaparsec (eof, errorBundlePretty, parse)
fastaParserSpec :: Spec
-fastaParserSpec = describe "Fasta format parser." $ do
+fastaParserSpec = describe "Fasta format parser" $ do
emptyFasta
onlyName
oneSequence
@@ -25,6 +26,7 @@ fastaParserSpec = describe "Fasta format parser." $ do
sequenceWithTabsInName
sequenceWithTabsInSequence
sequenceWithModifications
+ sequenceWithSpaces
toughParserTests
emptyFasta :: Spec
@@ -49,19 +51,22 @@ twoSequences :: Spec
twoSequences = describe "twoSequences" $ do
it "correctly parses two correct sequences" $ do
let res = parseOnly fastaP ">3HMX:A|PDBID|CHAIN|SEQUENCE\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSE\nVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL\n>7HMX:A|PDBID|CHAIN|SEQUENCE\nEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\nVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL"
- res `shouldBe` Right [FastaItem @Char "3HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL"), FastaItem @Char "7HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL")]
+ res `shouldBe` Right
+ [ FastaItem @Char "3HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL")
+ , FastaItem @Char "7HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL")
+ ]
sequenceWithDigit :: Spec
sequenceWithDigit = describe "sequenceWithDigit" $ do
it "correctly parses incorrect sequence with digit" $ do
- let res = parseOnly fastaP ">123\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEE4GITWTLDQSSE"
- res `shouldBe` Right [FastaItem @Char "123" (bareSequence "")]
+ let res = parseOnly (fastaP @Char) ">123\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEE4GITWTLDQSSE"
+ res `shouldBe` Left "input.fasta:2:34:\n |\n2 | IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEE4GITWTLDQSSE\n | ^^\nunexpected \"4G\"\nexpecting end of input, end of line, or letter\n"
sequenceWithWrongName :: Spec
sequenceWithWrongName = describe "sequenceWithWrongName" $ do
it "correctly parses incorrect sequence with wrong name" $ do
- let res = parseOnly fastaP "123\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE"
- res `shouldBe` Right ([] :: Fasta Char)
+ let res = parseOnly (fastaP @Char) "123\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE"
+ res `shouldBe` Left "input.fasta:1:1:\n |\n1 | 123\n | ^\nunexpected '1'\nexpecting '>' or end of input\n"
sequenceWithSpacesInName :: Spec
sequenceWithSpacesInName = describe "sequenceWithSpacesInName" $ do
@@ -71,15 +76,15 @@ sequenceWithSpacesInName = describe "sequenceWithSpacesInName" $ do
sequenceWithSeveralEndOfLine :: Spec
sequenceWithSeveralEndOfLine = describe "sequenceWithSeveralEndOfLine" $ do
- it "correctly parses sequence with several \n after name" $ do
- let res = parseOnly fastaP ">this is my sequence\n\n\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE"
- res `shouldBe` Right [FastaItem @Char "this is my sequence" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE")]
+ it "correctly parses sequence with several \\n after name" $ do
+ let res = parseOnly (fastaP @Char) ">this is my sequence\n\n\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE"
+ res `shouldBe` Right [FastaItem "this is my sequence" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE")]
sequenceWithSeveralEndOfLineInSequence :: Spec
sequenceWithSeveralEndOfLineInSequence = describe "sequenceWithSeveralEndOfLineInSequence" $ do
- it "correctly parses sequence with several \n between sequence parts" $ do
- let res = parseOnly fastaP ">this is my sequence\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE\n\n\nYYYYYYYYYYYYYYYYYYYYYYYY"
- res `shouldBe` Right [FastaItem @Char "this is my sequence" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSEYYYYYYYYYYYYYYYYYYYYYYYY")]
+ it "correctly parses sequence with several \\n between sequence parts" $ do
+ let res = parseOnly (fastaP @Char) ">this is my sequence\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE\n\n\nYYYYYYYYYYYYYYYYYYYYYYYY"
+ res `shouldBe` Right [FastaItem "this is my sequence" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSEYYYYYYYYYYYYYYYYYYYYYYYY")]
sequenceWithTabsInName :: Spec
sequenceWithTabsInName = describe "sequenceWithTabsInName" $ do
@@ -99,13 +104,22 @@ sequenceWithModifications = describe "sequenceWithModifications" $ do
let res = parseOnly fastaP ">this is my sequence\nIWEL[mU*]KKDVYV\t\t\nYY[56FAM]YY[Trololo]YY\t\n"
res `shouldBe` Right [FastaItem "this is my sequence" (bareSequence [Letter 'I', Letter 'W', Letter 'E', Letter 'L', Mod Mod_mU_Star, Letter 'K', Letter 'K', Letter 'D', Letter 'V', Letter 'Y', Letter 'V', Letter 'Y', Letter 'Y', Mod Mod_56FAM, Letter 'Y', Letter 'Y', Mod (Unknown "[Trololo]"), Letter 'Y', Letter 'Y'])]
+sequenceWithSpaces :: Spec
+sequenceWithSpaces = describe "sequenceWithSpaces" $ do
+ it "correctly parses sequence with spaces" $ do
+ let res = parseOnly fastaP ">test1\nAAAA TTTT GGGG ccA\n"
+ res `shouldBe` Right [FastaItem @Char "test1" (bareSequence "AAAATTTTGGGGccA")]
+
toughParserTests :: Spec
toughParserTests = describe "various parser tests" $ do
it "correctly parses empty lines" $ checkParser correctTest1 (Right correctAnswer)
it "correctly parses empty lines with spaces" $ checkParser correctTest2 (Right correctAnswer)
it "correctly parses empty lines with tabs" $ checkParser correctTest3 (Right correctAnswer)
- it "correctly fails to parse a name without >" $ checkParser incorrectTest1 (Left "endOfInput")
- it "correctly fails to parse a new sequence at the same line" $ checkParser incorrectTest2 (Left "endOfInput")
+ it "correctly parses empty lines with trailing tabs" $ checkParser correctTest4 (Right correctAnswer4)
+ it "correctly fails to parse a name without >" $ checkParser incorrectTest1
+ (Left "input.fasta:1:1:\n |\n1 | test1\n | ^\nunexpected 't'\nexpecting '>' or end of input\n")
+ it "correctly fails to parse a new sequence at the same line" $ checkParser incorrectTest2
+ (Left "input.fasta:3:8:\n |\n3 | GHIJKL >test2\n | ^^\nunexpected \">t\"\nexpecting end of input, end of line, or letter\n")
correctTest1 :: Text
correctTest1 = T.unlines
@@ -137,6 +151,14 @@ correctTest3 = T.unlines
, "ABCDEF"
]
+correctTest4 :: Text
+correctTest4 = "> test4\nTTTAGGTactTGT\t\t \t\n"
+
+correctAnswer4 :: [FastaItem Char]
+correctAnswer4 =
+ [ FastaItem "test4" (bareSequence "TTTAGGTactTGT")
+ ]
+
incorrectTest1 :: Text
incorrectTest1 = T.unlines
[ "test1"
@@ -157,5 +179,7 @@ incorrectTest2 = T.unlines
correctAnswer :: Fasta Char
correctAnswer = [FastaItem "test1" (bareSequence "ABCDEFGHIJKL"), FastaItem "test2" (bareSequence "ABCDEF")]
-checkParser :: Text -> Either String (Fasta Char) -> Expectation
-checkParser source expectation = parseOnly (fastaP <* endOfInput) source `shouldBe` expectation
+checkParser :: HasCallStack => Text -> Either String (Fasta Char) -> Expectation
+checkParser source expectation =
+ first errorBundlePretty (parse (fastaP <* eof) "input.fasta" source)
+ `shouldBe` expectation