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bioinformatics-toolkit 0.9.2 → 0.9.3

raw patch · 2 files changed

+15/−6 lines, 2 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

+ Bio.RealWorld.GENCODE: [transType] :: Transcript -> TranscriptType
+ Bio.RealWorld.GENCODE: instance GHC.Classes.Eq Bio.RealWorld.GENCODE.TranscriptType
+ Bio.RealWorld.GENCODE: instance GHC.Classes.Ord Bio.RealWorld.GENCODE.TranscriptType
+ Bio.RealWorld.GENCODE: instance GHC.Show.Show Bio.RealWorld.GENCODE.TranscriptType
- Bio.Data.Bed: _bed :: forall bed_aAAi a_aAAj bed_aALt. Lens (BEDExt bed_aAAi a_aAAj) (BEDExt bed_aALt a_aAAj) bed_aAAi bed_aALt
+ Bio.Data.Bed: _bed :: forall bed_aAFF a_aAFG bed_aAQQ. Lens (BEDExt bed_aAFF a_aAFG) (BEDExt bed_aAQQ a_aAFG) bed_aAFF bed_aAQQ
- Bio.Data.Bed: _data :: forall bed_aAAi a_aAAj a_aALu. Lens (BEDExt bed_aAAi a_aAAj) (BEDExt bed_aAAi a_aALu) a_aAAj a_aALu
+ Bio.Data.Bed: _data :: forall bed_aAFF a_aAFG a_aAQR. Lens (BEDExt bed_aAFF a_aAFG) (BEDExt bed_aAFF a_aAQR) a_aAFG a_aAQR
- Bio.Data.Bed.Types: _bed :: forall bed_aAAi a_aAAj bed_aALt. Lens (BEDExt bed_aAAi a_aAAj) (BEDExt bed_aALt a_aAAj) bed_aAAi bed_aALt
+ Bio.Data.Bed.Types: _bed :: forall bed_aAFF a_aAFG bed_aAQQ. Lens (BEDExt bed_aAFF a_aAFG) (BEDExt bed_aAQQ a_aAFG) bed_aAFF bed_aAQQ
- Bio.Data.Bed.Types: _data :: forall bed_aAAi a_aAAj a_aALu. Lens (BEDExt bed_aAAi a_aAAj) (BEDExt bed_aAAi a_aALu) a_aAAj a_aALu
+ Bio.Data.Bed.Types: _data :: forall bed_aAFF a_aAFG a_aAQR. Lens (BEDExt bed_aAFF a_aAFG) (BEDExt bed_aAFF a_aAQR) a_aAFG a_aAQR
- Bio.RealWorld.GENCODE: Transcript :: !ByteString -> !Int -> !Int -> !Bool -> ![(Int, Int)] -> ![(Int, Int)] -> Transcript
+ Bio.RealWorld.GENCODE: Transcript :: !ByteString -> !Int -> !Int -> !Bool -> ![(Int, Int)] -> ![(Int, Int)] -> TranscriptType -> Transcript

Files

bioinformatics-toolkit.cabal view
@@ -1,5 +1,5 @@ name:                bioinformatics-toolkit-version:             0.9.2+version:             0.9.3 synopsis:            A collection of bioinformatics tools description:         A collection of bioinformatics tools license:             MIT
src/Bio/RealWorld/GENCODE.hs view
@@ -19,6 +19,10 @@  import           Bio.Utils.Misc        (readInt) +data TranscriptType = Coding+                    | NonCoding+                    deriving (Show, Eq, Ord)+ -- | GTF's position is 1-based, but here we convert it to 0-based indexing. data Gene = Gene     { geneName        :: !(CI B.ByteString)@@ -37,6 +41,7 @@     , transStrand      :: !Bool     , transExon        :: ![(Int, Int)]     , transUTR         :: ![(Int, Int)]+    , transType        :: TranscriptType     } deriving (Show, Eq, Ord)  -- | Read gene information from Gencode GTF file@@ -72,17 +77,21 @@         | featType == "utr" = _4 %~ ((tid, utr):) $ acc         | otherwise = acc       where-        gene = Gene (mk $ getField "gene_name") gid chr lPos rPos (f7=="+") []-        transcript = Transcript tid lPos rPos (f7=="+") [] []+        gene = Gene (mk $ fromJust $ getField "gene_name") gid chr lPos rPos (f7=="+") []+        transcript = Transcript tid lPos rPos (f7=="+") [] [] tTy         exon = (lPos, rPos)         utr = (lPos, rPos)         [chr,_,f3,f4,f5,_,f7,_,f9] = B.split '\t' l-        gid = getField "gene_id"-        tid = getField "transcript_id"+        gid = fromJust $ getField "gene_id"+        tid = fromJust $ getField "transcript_id"+        tTy = case getField "transcript_type" of+            Just "protein_coding" -> Coding+            Nothing -> Coding+            _ -> NonCoding         lPos = readInt f4 - 1         rPos = readInt f5 - 1         featType = B.map toLower f3-        getField x = B.init $ B.drop 2 $ fromJust $ lookup x $+        getField x = fmap (B.init . B.drop 2) $ lookup x $             map (B.break isSpace . strip) $ B.split ';' f9     strip = fst . B.spanEnd isSpace . B.dropWhile isSpace     isSpace = (== ' ')