seqloc 0.6.1 → 0.6.1.1

raw patch · 3 files changed

+30/−6 lines, 3 filesPVP: minor bump suggested

API additions: PVP suggests at least a minor version bump

API changes (from Hackage documentation)

Files

• seqloc.cabal +1/−1
• src/Bio/SeqLoc/LocMap.hs +12/−5
• test/TestMain.hs +17/−0

@@ -1,5 +1,5 @@ Name:                seqloc-Version:             0.6.1+Version:             0.6.1.1 Cabal-Version:       >= 1.14 Synopsis:            Handle sequence locations for bioinformatics Description:         Handle sequence locations for bioinformatics

@@ -25,14 +25,14 @@   , Locatable(..)   , WithLocation(..)   , locatableSeqLocMap-  , queryLocatable, queryLocCompatible+  , queryLocatable, queryLocCompatible, queryLocInto        )        where  import qualified Data.HashMap.Strict as HM import Data.List--- import Data.Maybe+import Data.Maybe  import qualified Bio.SeqLoc.Location as Loc import Bio.SeqLoc.OnSeq@@ -171,8 +171,15 @@ -- | Retrieve a list of `Locatable` objects whose spliced structure -- contains the query location specifically. queryLocCompatible :: (Locatable o) => Maybe Strand -> SpliceSeqLoc -> SeqLocMap o -> [o]-queryLocCompatible mstr qyloc = filter compatHit . querySeqLoc qyloc-  where compatHit sb = maybe False strandCompat $ unOnSeq qyloc `SpLoc.locInto` (unOnSeq . locate $ sb)+queryLocCompatible mstr qyloc = map fst . queryLocInto mstr qyloc++-- | Retrieve a list of `Locatable` objects whose splice structure+-- contains the query location, paired with the sub-location of the+-- query within the `Locatable`.+queryLocInto :: (Locatable o) => Maybe Strand -> SpliceSeqLoc -> SeqLocMap o -> [(o, SpLoc.SpliceLoc)]+queryLocInto mstr qyloc = filter strandCompat . mapMaybe compatHit . querySeqLoc qyloc+  where compatHit sb = do into <- unOnSeq qyloc `SpLoc.locInto` (unOnSeq . locate $ sb)+                          return (sb, into)         strandCompat = case mstr of           Nothing -> const True-          Just s -> (== s) . Loc.strand +          Just s -> (== s) . Loc.strand . snd

@@ -51,6 +51,7 @@         , T "Locatable hit Spliced Extended" property_Locatable_locHitSpliced         , T "Locatable compat Contig Ext'd"  property_Locatable_locCompatContig         , T "Locatable compat Spliced Ext'd" property_Locatable_locCompatSpliced+        , T "Locatable into"                 property_Locatable_locInto                    , T "Pos revCompl"                  test_Pos_revCompl         , T "Pos atPos"                     property_Pos_atPos@@ -587,6 +588,22 @@                   , zipWith (\isin hit -> hit == isin) isInRevs revHits                   , zipWith (\isin hit -> hit == isin) isIns allHits                   ]++property_Locatable_locInto :: [SpLoc.SpliceLoc] -> SpLoc.SpliceLoc -> Property+property_Locatable_locInto ls qy =+  (not . null $ ls) ==> +  forAll genPositiveOffset $ \binsz ->+  forAll genName $ \chr ->+  forAll (elements ls) $ \target -> +  case qy `SpLoc.locOutof` target of+    Nothing -> True+    Just targout -> let seqlocs = map (OnSeq chr) ls+                        locables = [ LM.WithLocation sl sl | sl <- seqlocs ]+                        slm = LM.locatableSeqLocMap binsz locables+                        intos = LM.queryLocInto Nothing (OnSeq chr targout) slm+                    in case filter ((== target) . unOnSeq . LM.withoutLocation . fst) intos of+                      [] -> False+                      ontargets -> and $ map ((== qy) . snd) ontargets  instance (Arbitrary a) => Arbitrary (OnSeq a) where   arbitrary = OnSeq <$> arbitrary <*> arbitrary