fasta 0.7.2.0 → 0.7.2.1

raw patch · 6 files changed

+22/−12 lines, 6 filesdep ~foldlPVP ok

version bump matches the API change (PVP)

Dependency ranges changed: foldl

API changes (from Hackage documentation)

Files

• fasta.cabal +2/−2
• src/Data/Fasta/ByteString/Lazy/Translation.hs +4/−2
• src/Data/Fasta/ByteString/Translation.hs +4/−2
• src/Data/Fasta/String/Translation.hs +4/−2
• src/Data/Fasta/Text/Lazy/Translation.hs +4/−2
• src/Data/Fasta/Text/Translation.hs +4/−2

@@ -10,7 +10,7 @@ -- PVP summary:      +-+------- breaking API changes --                   | | +----- non-breaking API additions --                   | | | +--- code changes with no API change-version:             0.7.2.0+version:             0.7.2.1  -- A short (one-line) description of the package. synopsis:            A simple, mindless parser for fasta files.@@ -83,7 +83,7 @@                        pipes-text >= 0.0 && < 0.1,                        pipes-bytestring >= 2.1 && < 2.2,                        lens >= 4.9 && < 4.12,-                       foldl >= 1.0 && < 1.1+                       foldl >= 1.0 && < 1.2      -- Directories containing source files.   hs-source-dirs:      src

@@ -30,6 +30,7 @@  -- | Converts a codon to an amino acid -- Remember, if there is an "N" in that DNA sequence, then it is invalid+-- and treated as a gap codon2aa :: Codon -> Either BL.ByteString BL.ByteString codon2aa x     | codon `elem` ["GCT", "GCC", "GCA", "GCG"]               = Right "A"@@ -63,8 +64,9 @@     codon    = BL.map toUpper x     errorMsg = BL.append "Unidentified codon: " codon --- | Translates a string of nucleotides. Returns a text with the error if the--- codon is invalid.+-- | Translates a bytestring of nucleotides given a reading frame (1, 2, or+-- 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns+-- a bytestring with the error if the codon is invalid. translate :: Int64 -> FastaSequence -> Either BL.ByteString FastaSequence translate pos x     | any isLeft' translation = Left $ head . lefts $ translation

@@ -29,6 +29,7 @@  -- | Converts a codon to an amino acid -- Remember, if there is an "N" in that DNA sequence, then it is invalid+-- and treated as a gap codon2aa :: Codon -> Either B.ByteString B.ByteString codon2aa x     | codon `elem` ["GCT", "GCC", "GCA", "GCG"]               = Right "A"@@ -62,8 +63,9 @@     codon    = B.map toUpper x     errorMsg = B.append "Unidentified codon: " codon --- | Translates a string of nucleotides. Returns a text with the error if the--- codon is invalid.+-- | Translates a bytestring of nucleotides given a reading frame (1, 2, or+-- 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns+-- a bytestring with the error if the codon is invalid. translate :: Int -> FastaSequence -> Either B.ByteString FastaSequence translate pos x     | any isLeft' translation = Left $ head . lefts $ translation

@@ -19,6 +19,7 @@  -- | Converts a codon to an amino acid -- Remember, if there is an "N" in that DNA sequence, then it is invalid+-- and treated as a gap codon2aa :: Codon -> Either String Char codon2aa x     | codon `elem` ["GCT", "GCC", "GCA", "GCG"]               = Right 'A'@@ -52,8 +53,9 @@     codon    = map toUpper x     errorMsg = "Unidentified codon: " ++ codon --- | Translates a string of nucleotides. Returns a string with the error if the--- codon is invalid.+-- | Translates a string of nucleotides given a reading frame (1, 2, or+-- 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns+-- a string with the error if the codon is invalid. translate :: Int -> FastaSequence -> Either String FastaSequence translate pos x     | any isLeft' translation = Left $ head . lefts $ translation

@@ -20,6 +20,7 @@  -- | Converts a codon to an amino acid -- Remember, if there is an "N" in that DNA sequence, then it is invalid+-- and treated as a gap codon2aa :: Codon -> Either T.Text T.Text codon2aa x     | codon `elem` ["GCT", "GCC", "GCA", "GCG"]               = Right "A"@@ -53,8 +54,9 @@     codon    = T.toUpper x     errorMsg = T.append "Unidentified codon: " codon --- | Translates a string of nucleotides. Returns a text with the error if the--- codon is invalid.+-- | Translates a text of nucleotides given a reading frame (1, 2, or+-- 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns+-- a text with the error if the codon is invalid. translate :: Int64 -> FastaSequence -> Either T.Text FastaSequence translate pos x     | any isLeft' translation = Left $ head . lefts $ translation

@@ -19,6 +19,7 @@  -- | Converts a codon to an amino acid -- Remember, if there is an "N" in that DNA sequence, then it is invalid+-- and treated as a gap codon2aa :: Codon -> Either T.Text T.Text codon2aa x     | codon `elem` ["GCT", "GCC", "GCA", "GCG"]               = Right "A"@@ -52,8 +53,9 @@     codon    = T.toUpper x     errorMsg = T.append "Unidentified codon: " codon --- | Translates a string of nucleotides. Returns a text with the error if the--- codon is invalid.+-- | Translates a text of nucleotides given a reading frame (1, 2, or+-- 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns+-- a text with the error if the codon is invalid. translate :: Int -> FastaSequence -> Either T.Text FastaSequence translate pos x     | any isLeft' translation = Left $ head . lefts $ translation