diff --git a/seqloc-datafiles.cabal b/seqloc-datafiles.cabal --- a/seqloc-datafiles.cabal +++ b/seqloc-datafiles.cabal @@ -1,5 +1,5 @@ Name: seqloc-datafiles -Version: 0.1.1 +Version: 0.2 Cabal-Version: >= 1.4 Synopsis: Read and write BED and GTF format genome annotations Description: Read and write BED and GTF format genome annotations @@ -20,7 +20,7 @@ Other-modules: Bio.SeqLoc.ZeptoUtils Build-depends: base >= 4.2 && < 5, bytestring, haskell98, attoparsec >= 0.8.5, hashable, unordered-containers, - iteratee >= 0.8.1, seqloc >= 0.0 + iteratee >= 0.8.1, seqloc >= 0.3.1, biocore Hs-Source-Dirs: src Ghc-options: -Wall @@ -29,7 +29,7 @@ Other-modules: Bio.SeqLoc.GTF, Bio.SeqLoc.Bed, Bio.SeqLoc.ZeptoUtils Build-depends: base >= 4.2 && < 5, bytestring, haskell98, attoparsec >= 0.8.5, hashable, unordered-containers, - iteratee >= 0.8.1, seqloc >= 0.0, transformers, monads-tf + iteratee >= 0.8.1, seqloc >= 0.3.1, biocore, transformers, monads-tf Hs-Source-Dirs: src Ghc-options: -Wall -rtsopts C-Sources: src/rtsopts.c @@ -41,7 +41,7 @@ Other-modules: Bio.SeqLoc.GTF, Bio.SeqLoc.TranscriptTable, Bio.SeqLoc.ZeptoUtils Build-depends: base >= 4.2 && < 5, bytestring, haskell98, attoparsec >= 0.8.5, hashable, unordered-containers, - iteratee >= 0.8.1, seqloc >= 0.0, + iteratee >= 0.8.1, seqloc >= 0.3.1, biocore, QuickCheck, random Hs-Source-Dirs: src, test Ghc-options: -Wall -rtsopts @@ -54,7 +54,7 @@ Other-modules: Bio.SeqLoc.Bed, Bio.SeqLoc.TranscriptTable, Bio.SeqLoc.ZeptoUtils Build-depends: base >= 4.2 && < 5, bytestring, haskell98, attoparsec >= 0.8.5, hashable, unordered-containers, - iteratee >= 0.8.1, seqloc >= 0.0, + iteratee >= 0.8.1, seqloc >= 0.3.1, biocore, QuickCheck, random Hs-Source-Dirs: src, test Ghc-options: -Wall @@ -66,7 +66,7 @@ Other-modules: Bio.SeqLoc.GTF, Bio.SeqLoc.TranscriptTable, Bio.SeqLoc.ZeptoUtils Build-depends: base >= 4.2 && < 5, bytestring, haskell98, attoparsec >= 0.8.5, hashable, unordered-containers, - iteratee >= 0.8.1, seqloc >= 0.0, + iteratee >= 0.8.1, seqloc >= 0.3.1, biocore, QuickCheck, random Hs-Source-Dirs: src, test Ghc-options: -Wall -rtsopts diff --git a/src/Bio/SeqLoc/Bed.hs b/src/Bio/SeqLoc/Bed.hs --- a/src/Bio/SeqLoc/Bed.hs +++ b/src/Bio/SeqLoc/Bed.hs @@ -40,10 +40,10 @@ -> BS.ByteString transcriptToBed score rgb trx = unfields fields where unfields = BS.intercalate (BS.singleton '\t') - fields = [ unSeqName chrom + fields = [ unSeqLabel chrom , repr $ chromStart , repr $ chromEnd + 1 - , unSeqName . trxId $ trx + , unSeqLabel . trxId $ trx , score , strandchr , repr $ thickStart @@ -55,7 +55,7 @@ ] (OnSeq chrom loc) = location trx (chromStart, chromEnd) = Loc.bounds loc - strandchr = case Loc.strand loc of Fwd -> "+"; RevCompl -> "-" + strandchr = case Loc.strand loc of Plus -> "+"; Minus -> "-" (thickStart, thickEnd) = maybe noCds (Loc.bounds . unOnSeq) . cdsLocation $ trx noCds = (chromStart, chromStart - 1) contigs = sortBy (comparing Loc.offset5) . Loc.toContigs $ loc @@ -119,21 +119,21 @@ cdsloc <- if thickStart >= thickEnd then return Nothing else liftM Just $! bedCdsLoc loc thickStart thickEnd - let n = SeqName $ BS.copy name - c = SeqName $ BS.copy chrom + let n = toSeqLabel $ BS.copy name + c = toSeqLabel $ BS.copy chrom return $! Transcript n n (OnSeq c loc) cdsloc bedTrxLoc :: (Monad m) => Pos.Offset -> Pos.Offset -> Strand -> [(Pos.Offset, Pos.Offset)] -> m SpLoc.SpliceLoc bedTrxLoc chromStart chromEnd str = maybe badContigs (return . stranded str) . SpLoc.fromContigs . map blockContig - where blockContig (bsize, bstart) = Loc.fromPosLen (Pos.Pos (chromStart + bstart) Fwd) bsize + where blockContig (bsize, bstart) = Loc.fromPosLen (Pos.Pos (chromStart + bstart) Plus) bsize badContigs = fail $ "Bio.SeqLoc.Bed: bad blocks in " ++ show (chromStart, chromEnd) bedCdsLoc :: (Monad m) => SpLoc.SpliceLoc -> Pos.Offset -> Pos.Offset -> m Loc.ContigLoc bedCdsLoc loc thickStart thickEnd = maybe badCdsLoc return $ do - relstart <- Loc.posInto (Pos.Pos thickStart Fwd) loc - relend <- Loc.posInto (Pos.Pos (thickEnd - 1) Fwd) loc + relstart <- Loc.posInto (Pos.Pos thickStart Plus) loc + relend <- Loc.posInto (Pos.Pos (thickEnd - 1) Plus) loc return $! stranded (Loc.strand loc) $ Loc.fromStartEnd (Pos.offset relstart) (Pos.offset relend) where badCdsLoc = fail $ "Bio.SeqLoc.Bed: bad cds in " ++ (BS.unpack . BS.unwords $ [ repr loc, repr thickStart, repr thickEnd ]) diff --git a/src/Bio/SeqLoc/GTF.hs b/src/Bio/SeqLoc/GTF.hs --- a/src/Bio/SeqLoc/GTF.hs +++ b/src/Bio/SeqLoc/GTF.hs @@ -43,20 +43,20 @@ splocLines src trx ftype (OnSeq refname sploc) = map contigLines . Loc.toContigs $ sploc where contigLines contig = let (start0, end0) = Loc.bounds contig strchr = case Loc.strand contig of - Fwd -> "+" - RevCompl -> "-" - in unfields [ unSeqName refname + Plus -> "+" + Minus -> "-" + in unfields [ unSeqLabel refname , src , ftype - , BS.pack . show . Pos.unOffset . (+ 1) $ start0 - , BS.pack . show . Pos.unOffset . (+ 1) $ end0 + , BS.pack . show . Pos.unOff . (+ 1) $ start0 + , BS.pack . show . Pos.unOff . (+ 1) $ end0 , "0.0" , strchr , "." , attrs ] - attrs = BS.concat [ "gene_id \"", unSeqName . geneId $ trx - , "\"; transcript_id \"", unSeqName . trxId $ trx + attrs = BS.concat [ "gene_id \"", unSeqLabel . geneId $ trx + , "\"; transcript_id \"", unSeqLabel . trxId $ trx , "\"; " ] unfields = BS.intercalate (BS.singleton '\t') @@ -106,7 +106,7 @@ mkTranscript :: BS.ByteString -> [ContigSeqLoc] -> [ContigSeqLoc] -> BS.ByteString -> Either String Transcript mkTranscript trx exons cdses gene = moderr $ do loc <- exonLoc exons cdsloc <- cdsLoc loc cdses - return $ Transcript (SeqName gene) (SeqName trx) loc cdsloc + return $ Transcript (toSeqLabel gene) (toSeqLabel trx) loc cdsloc where moderr = either (Left . (("Transcript " ++ show trx ++ ": ") ++)) Right exonLoc :: [ContigSeqLoc] -> Either String SpliceSeqLoc @@ -122,7 +122,9 @@ cdsLoc _ [] = return Nothing cdsLoc (OnSeq trxname trxloc) cdses@(_:_) = do (seqname, rawcontigs) <- allSameName cdses - when (trxname /= seqname) $ Left . unwords $ [ "CDS sequence name mismatch", show trxname, show seqname ] + when (trxname /= seqname) $ Left . unwords $ [ "CDS sequence name mismatch", + show $ unSeqLabel trxname + , show $ unSeqLabel seqname ] contigs <- sortclocs rawcontigs (contigIn0:contigInRest) <- mapM (cdsIntoTranscript trxloc) contigs cloc <- foldM mergeCLocs contigIn0 contigInRest @@ -139,7 +141,7 @@ mergeCLocs :: Loc.ContigLoc -> Loc.ContigLoc -> Either String Loc.ContigLoc mergeCLocs cloc0 clocnext - | (Loc.strand cloc0 == Fwd) && (Loc.startPos clocnext == Loc.endPos cloc0 `Pos.slide` 1) + | (Loc.strand cloc0 == Plus) && (Loc.startPos clocnext == Loc.endPos cloc0 `Pos.slide` 1) = return $! Loc.extend (0, Loc.length clocnext) cloc0 | otherwise = Left . unwords $ [ "Merging non-adjacent contigs: " , BS.unpack . repr $ cloc0 @@ -147,16 +149,16 @@ ] -allSameName :: [OnSeq a] -> Either String (SeqName, [a]) -allSameName s = case group . map onSeqName $ s of +allSameName :: [OnSeq a] -> Either String (SeqLabel, [a]) +allSameName s = case group . map onSeqLabel $ s of [(name0:_)] -> return (name0, map unOnSeq s) - names -> Left $ "allSameName: names " ++ show (map (unSeqName . head) names) + names -> Left $ "allSameName: names " ++ show (map (unSeqLabel . head) names) -data GtfLine = GtfLine { gtfGene, gtfTrx, gtfFtype :: !BS.ByteString, gtfLoc :: !ContigSeqLoc } deriving (Show) +data GtfLine = GtfLine { gtfGene, gtfTrx, gtfFtype :: !BS.ByteString, gtfLoc :: !ContigSeqLoc } data GtfTrxs = GtfTrxs { gtfExonLocs, gtfCdsLocs :: !(HM.HashMap BS.ByteString [ContigSeqLoc]) , gtfTogene :: !(HM.HashMap BS.ByteString BS.ByteString) - } deriving (Show) + } ftypeCds :: BS.ByteString ftypeCds = BS.pack "CDS" @@ -190,7 +192,7 @@ _frame <- dropField gene <- attr "gene_id" trx <- attr "transcript_id" - let name = SeqName . BS.copy $ seqname + let name = toSeqLabel . BS.copy $ seqname loc = Loc.fromBoundsStrand (start - 1) (end - 1) str return $! GtfLine gene trx ftype (OnSeq name loc) diff --git a/src/Bio/SeqLoc/TranscriptTable.hs b/src/Bio/SeqLoc/TranscriptTable.hs --- a/src/Bio/SeqLoc/TranscriptTable.hs +++ b/src/Bio/SeqLoc/TranscriptTable.hs @@ -29,7 +29,7 @@ cdsloc <- if cdslocstr == na then return Nothing else liftM Just $! unreprMaybe cdslocstr - return $! Transcript (SeqName . BS.copy $ geneid) (SeqName . BS.copy $ trxid) trxloc cdsloc + return $! Transcript (toSeqLabel . BS.copy $ geneid) (toSeqLabel . BS.copy $ trxid) trxloc cdsloc _ -> Nothing -- | Write a transcript table file @@ -38,8 +38,8 @@ -- | Produce a single transcript table line for a 'Transcript', newline not included. unparseLine :: Transcript -> BS.ByteString -unparseLine trx = BS.intercalate (BS.singleton '\t') $ [ unSeqName . geneId $ trx - , unSeqName . trxId $ trx +unparseLine trx = BS.intercalate (BS.singleton '\t') $ [ unSeqLabel . geneId $ trx + , unSeqLabel . trxId $ trx , repr . location $ trx , maybe na repr . cds $ trx ] diff --git a/src/Bio/SeqLoc/ZeptoUtils.hs b/src/Bio/SeqLoc/ZeptoUtils.hs --- a/src/Bio/SeqLoc/ZeptoUtils.hs +++ b/src/Bio/SeqLoc/ZeptoUtils.hs @@ -14,8 +14,8 @@ import Bio.SeqLoc.Strand strand :: ZP.Parser Strand -strand = ((ZP.string "+\t" *> return Fwd) <|> - (ZP.string "-\t" *> return RevCompl)) +strand = ((ZP.string "+\t" *> return Plus) <|> + (ZP.string "-\t" *> return Minus)) decfield :: (Integral a) => ZP.Parser a decfield = decimal <* ZP.string "\t" diff --git a/src/GtfToBed.hs b/src/GtfToBed.hs --- a/src/GtfToBed.hs +++ b/src/GtfToBed.hs @@ -32,7 +32,7 @@ mapM_ (BS.hPutStrLn h . transcriptToBedStd) trxs adjustStop = if confStopIncluded conf then removeDoubleStop else id removeDoubleStop trx = trx { cds = cds trx >>= shortenLoc } - shortenLoc l = Loc.clocOutof (Loc.fromBoundsStrand 0 end Fwd) l + shortenLoc l = Loc.clocOutof (Loc.fromBoundsStrand 0 end Plus) l where end = max 0 $ Loc.length l - 4 handleErrors (trxs, errs) = do maybe putErrs filePutErrs $ confBadTranscripts conf return trxs diff --git a/test/GtfIntrons.hs b/test/GtfIntrons.hs --- a/test/GtfIntrons.hs +++ b/test/GtfIntrons.hs @@ -34,8 +34,8 @@ transcriptIntrons trx = zipWith intronTranscript [1..] . junctions $ sploc where (OnSeq refname sploc) = location trx intronTranscript idx jct = Transcript geneid trxid loc Nothing - where geneid = SeqName . flip BS.append "_introns" . unSeqName . geneId $ trx - trxid = SeqName . flip BS.append trxsuffix . unSeqName . trxId $ trx + where geneid = toSeqLabel . flip BS.append "_introns" . unSeqLabel . geneId $ trx + trxid = toSeqLabel . flip BS.append trxsuffix . unSeqLabel . trxId $ trx trxsuffix = "_intron" `BS.append` (BS.pack . show $ idx) loc = OnSeq refname (fromMaybe noLoc $ SpLoc.fromContigs [ intron jct ]) noLoc = error $ "Unable to create singleton SpLoc from " ++ (BS.unpack . repr) jct