Bio.Data.Bed

Documentation

class BEDLike b where

A class representing BED-like data, e.g., BED3, BED6 and BED12. BED format uses 0-based index (see documentation).

Minimal complete definition

chrom, chromStart, chromEnd, name, score, strand

Methods

chrom :: Lens' b ByteString

Field lens

chromStart :: Lens' b Int

chromEnd :: Lens' b Int

name :: Lens' b (Maybe ByteString)

score :: Lens' b (Maybe Double)

strand :: Lens' b (Maybe Bool)

size :: b -> Int

Return the size of a bed region.

Instances

BEDLike NarrowPeak

Methods

chrom :: Lens' NarrowPeak ByteString

chromStart :: Lens' NarrowPeak Int

chromEnd :: Lens' NarrowPeak Int

name :: Lens' NarrowPeak (Maybe ByteString)

score :: Lens' NarrowPeak (Maybe Double)

strand :: Lens' NarrowPeak (Maybe Bool)

size :: NarrowPeak -> Int

BEDLike BED3

Methods

chrom :: Lens' BED3 ByteString

chromStart :: Lens' BED3 Int

chromEnd :: Lens' BED3 Int

name :: Lens' BED3 (Maybe ByteString)

score :: Lens' BED3 (Maybe Double)

strand :: Lens' BED3 (Maybe Bool)

size :: BED3 -> Int

BEDLike BED

Methods

chrom :: Lens' BED ByteString

chromStart :: Lens' BED Int

chromEnd :: Lens' BED Int

name :: Lens' BED (Maybe ByteString)

score :: Lens' BED (Maybe Double)

strand :: Lens' BED (Maybe Bool)

size :: BED -> Int

BEDLike bed => BEDLike (BEDExt bed a)

Methods

chrom :: Lens' (BEDExt bed a) ByteString

chromStart :: Lens' (BEDExt bed a) Int

chromEnd :: Lens' (BEDExt bed a) Int

name :: Lens' (BEDExt bed a) (Maybe ByteString)

score :: Lens' (BEDExt bed a) (Maybe Double)

strand :: Lens' (BEDExt bed a) (Maybe Bool)

size :: BEDExt bed a -> Int

class BEDLike b => BEDConvert b where

Minimal complete definition

asBed, fromLine, toLine

Methods

asBed :: ByteString -> Int -> Int -> b

Construct bed record from chromsomoe, start location and end location

fromLine :: ByteString -> b

Convert bytestring to bed format

toLine :: b -> ByteString

Convert bed to bytestring

convert :: BEDLike b' => b' -> b

Instances

BEDConvert NarrowPeak

Methods

asBed :: ByteString -> Int -> Int -> NarrowPeak

fromLine :: ByteString -> NarrowPeak

toLine :: NarrowPeak -> ByteString

convert :: BEDLike b' => b' -> NarrowPeak

BEDConvert BED3

Methods

asBed :: ByteString -> Int -> Int -> BED3

fromLine :: ByteString -> BED3

toLine :: BED3 -> ByteString

convert :: BEDLike b' => b' -> BED3

BEDConvert BED

Methods

asBed :: ByteString -> Int -> Int -> BED

fromLine :: ByteString -> BED

toLine :: BED -> ByteString

convert :: BEDLike b' => b' -> BED

(Default a, Read a, Show a, BEDConvert bed) => BEDConvert (BEDExt bed a)

Methods

asBed :: ByteString -> Int -> Int -> BEDExt bed a

fromLine :: ByteString -> BEDExt bed a

toLine :: BEDExt bed a -> ByteString

convert :: BEDLike b' => b' -> BEDExt bed a

data BED

BED6 format, as described in http://genome.ucsc.edu/FAQ/FAQformat.html#format1.7

Instances

Eq BED

Methods

(==) :: BED -> BED -> Bool

(/=) :: BED -> BED -> Bool

Ord BED

Methods

compare :: BED -> BED -> Ordering

(<) :: BED -> BED -> Bool

(<=) :: BED -> BED -> Bool

(>) :: BED -> BED -> Bool

(>=) :: BED -> BED -> Bool

max :: BED -> BED -> BED

min :: BED -> BED -> BED

Read BED

Methods

readsPrec :: Int -> ReadS BED

readList :: ReadS [BED]

readPrec :: ReadPrec BED

readListPrec :: ReadPrec [BED]

Show BED

Methods

showsPrec :: Int -> BED -> ShowS

show :: BED -> String

showList :: [BED] -> ShowS

BEDConvert BED

Methods

asBed :: ByteString -> Int -> Int -> BED

fromLine :: ByteString -> BED

toLine :: BED -> ByteString

convert :: BEDLike b' => b' -> BED

BEDLike BED

Methods

chrom :: Lens' BED ByteString

chromStart :: Lens' BED Int

chromEnd :: Lens' BED Int

name :: Lens' BED (Maybe ByteString)

score :: Lens' BED (Maybe Double)

strand :: Lens' BED (Maybe Bool)

size :: BED -> Int

data BED3

Instances

Eq BED3

Methods

(==) :: BED3 -> BED3 -> Bool

(/=) :: BED3 -> BED3 -> Bool

Ord BED3

Methods

compare :: BED3 -> BED3 -> Ordering

(<) :: BED3 -> BED3 -> Bool

(<=) :: BED3 -> BED3 -> Bool

(>) :: BED3 -> BED3 -> Bool

(>=) :: BED3 -> BED3 -> Bool

max :: BED3 -> BED3 -> BED3

min :: BED3 -> BED3 -> BED3

Read BED3

Methods

readsPrec :: Int -> ReadS BED3

readList :: ReadS [BED3]

readPrec :: ReadPrec BED3

readListPrec :: ReadPrec [BED3]

Show BED3

Methods

showsPrec :: Int -> BED3 -> ShowS

show :: BED3 -> String

showList :: [BED3] -> ShowS

BEDConvert BED3

Methods

asBed :: ByteString -> Int -> Int -> BED3

fromLine :: ByteString -> BED3

toLine :: BED3 -> ByteString

convert :: BEDLike b' => b' -> BED3

BEDLike BED3

Methods

chrom :: Lens' BED3 ByteString

chromStart :: Lens' BED3 Int

chromEnd :: Lens' BED3 Int

name :: Lens' BED3 (Maybe ByteString)

score :: Lens' BED3 (Maybe Double)

strand :: Lens' BED3 (Maybe Bool)

size :: BED3 -> Int

data NarrowPeak

ENCODE narrowPeak format: https://genome.ucsc.edu/FAQ/FAQformat.html#format12

Instances

Eq NarrowPeak

Methods

(==) :: NarrowPeak -> NarrowPeak -> Bool

(/=) :: NarrowPeak -> NarrowPeak -> Bool

Read NarrowPeak

Methods

readsPrec :: Int -> ReadS NarrowPeak

readList :: ReadS [NarrowPeak]

readPrec :: ReadPrec NarrowPeak

readListPrec :: ReadPrec [NarrowPeak]

Show NarrowPeak

Methods

showsPrec :: Int -> NarrowPeak -> ShowS

show :: NarrowPeak -> String

showList :: [NarrowPeak] -> ShowS

BEDConvert NarrowPeak

Methods

asBed :: ByteString -> Int -> Int -> NarrowPeak

fromLine :: ByteString -> NarrowPeak

toLine :: NarrowPeak -> ByteString

convert :: BEDLike b' => b' -> NarrowPeak

BEDLike NarrowPeak

Methods

chrom :: Lens' NarrowPeak ByteString

chromStart :: Lens' NarrowPeak Int

chromEnd :: Lens' NarrowPeak Int

name :: Lens' NarrowPeak (Maybe ByteString)

score :: Lens' NarrowPeak (Maybe Double)

strand :: Lens' NarrowPeak (Maybe Bool)

size :: NarrowPeak -> Int

npSignal :: Lens' NarrowPeak Double

npPvalue :: Lens' NarrowPeak (Maybe Double)

npQvalue :: Lens' NarrowPeak (Maybe Double)

npPeak :: Lens' NarrowPeak (Maybe Int)

data BEDExt bed a

Constructors

BEDExt

Fields

• _ext_bed :: bed
• _ext_data :: a

Instances

(Eq a, Eq bed) => Eq (BEDExt bed a)

Methods

(==) :: BEDExt bed a -> BEDExt bed a -> Bool

(/=) :: BEDExt bed a -> BEDExt bed a -> Bool

(Read a, Read bed) => Read (BEDExt bed a)

Methods

readsPrec :: Int -> ReadS (BEDExt bed a)

readList :: ReadS [BEDExt bed a]

readPrec :: ReadPrec (BEDExt bed a)

readListPrec :: ReadPrec [BEDExt bed a]

(Show a, Show bed) => Show (BEDExt bed a)

Methods

showsPrec :: Int -> BEDExt bed a -> ShowS

show :: BEDExt bed a -> String

showList :: [BEDExt bed a] -> ShowS

(Default a, Read a, Show a, BEDConvert bed) => BEDConvert (BEDExt bed a)

Methods

asBed :: ByteString -> Int -> Int -> BEDExt bed a

fromLine :: ByteString -> BEDExt bed a

toLine :: BEDExt bed a -> ByteString

convert :: BEDLike b' => b' -> BEDExt bed a

BEDLike bed => BEDLike (BEDExt bed a)

Methods

chrom :: Lens' (BEDExt bed a) ByteString

chromStart :: Lens' (BEDExt bed a) Int

chromEnd :: Lens' (BEDExt bed a) Int

name :: Lens' (BEDExt bed a) (Maybe ByteString)

score :: Lens' (BEDExt bed a) (Maybe Double)

strand :: Lens' (BEDExt bed a) (Maybe Bool)

size :: BEDExt bed a -> Int

_bed :: forall bed a bed. Lens (BEDExt bed a) (BEDExt bed a) bed bed

_data :: forall bed a a. Lens (BEDExt bed a) (BEDExt bed a) a a

type BEDTree a = HashMap ByteString (IntervalMap Int a)

bedToTree :: BEDLike b => (a -> a -> a) -> [(b, a)] -> BEDTree a

sortedBedToTree :: (BEDLike b, Foldable f) => (a -> a -> a) -> Sorted (f (b, a)) -> BEDTree a

Convert a set of sorted bed records to interval tree, with combining function for equal keys.

intersecting :: BEDLike b => BEDTree a -> b -> IntervalMap Int a

isIntersected :: BEDLike b => BEDTree a -> b -> Bool

sizeOverlapped :: (BEDLike b1, BEDLike b2) => b1 -> b2 -> Int

splitBed :: BEDConvert b => Int -> b -> [b]

split a bed region into k consecutive subregions, discarding leftovers

splitBedBySize :: BEDConvert b => Int -> b -> [b]

split a bed region into consecutive fixed size subregions, discarding leftovers

splitBedBySizeLeft :: BEDConvert b => Int -> b -> [b]

split a bed region into consecutive fixed size subregions, including leftovers

splitBedBySizeOverlap

Arguments

:: BEDConvert b

=> Int

bin size

-> Int

overlap size

-> b

-> [b]

newtype Sorted b

a type to imply that underlying data structure is sorted

Constructors

Sorted

Fields

• fromSorted :: b

Instances

Eq b => Eq (Sorted b)

Methods

(==) :: Sorted b -> Sorted b -> Bool

(/=) :: Sorted b -> Sorted b -> Bool

Read b => Read (Sorted b)

Methods

readsPrec :: Int -> ReadS (Sorted b)

readList :: ReadS [Sorted b]

readPrec :: ReadPrec (Sorted b)

readListPrec :: ReadPrec [Sorted b]

Show b => Show (Sorted b)

Methods

showsPrec :: Int -> Sorted b -> ShowS

show :: Sorted b -> String

showList :: [Sorted b] -> ShowS

sortBed :: BEDLike b => [b] -> Sorted (Vector b)

sort BED, first by chromosome (alphabetical order), then by chromStart, last by chromEnd

intersectBed :: (BEDLike b1, BEDLike b2, Monad m) => [b2] -> ConduitT b1 b1 m ()

return records in A that are overlapped with records in B

intersectBedWith :: (BEDLike b1, BEDLike b2, Monad m) => (b1 -> [b2] -> a) -> [b2] -> ConduitT b1 a m ()

intersectSortedBed :: (BEDLike b1, BEDLike b2, Monad m) => Sorted (Vector b2) -> ConduitT b1 b1 m ()

return records in A that are overlapped with records in B

intersectSortedBedWith :: (BEDLike b1, BEDLike b2, Monad m) => (b1 -> [b2] -> a) -> Sorted (Vector b2) -> ConduitT b1 a m ()

isOverlapped :: (BEDLike b1, BEDLike b2) => b1 -> b2 -> Bool

mergeBed :: (BEDConvert b, Monad m) => [b] -> ConduitT i b m ()

mergeBedWith :: (BEDLike b, Monad m) => ([b] -> a) -> [b] -> ConduitT i a m ()

mergeSortedBed :: (BEDConvert b, Monad m) => Sorted (Vector b) -> ConduitT i b m ()

mergeSortedBedWith :: (BEDLike b, Monad m) => ([b] -> a) -> Sorted (Vector b) -> ConduitT i a m ()

splitOverlapped :: BEDLike b => ([b] -> a) -> [b] -> [(BED3, a)]

Split overlapped regions into non-overlapped regions. The input must be overlapped. This function is usually used with mergeBedWith.

hReadBed :: (BEDConvert b, MonadIO m) => Handle -> ConduitT i b m ()

Read records from a bed file handler in a streaming fashion.

hReadBed' :: (BEDConvert b, MonadIO m) => Handle -> m [b]

Non-streaming version.

readBed :: (BEDConvert b, MonadIO m) => FilePath -> ConduitT i b m ()

Read records from a bed file in a streaming fashion.

readBed' :: (BEDConvert b, MonadIO m) => FilePath -> m [b]

Non-streaming version.

hWriteBed :: (BEDConvert b, MonadIO m) => Handle -> ConduitT b o m ()

hWriteBed' :: (BEDConvert b, MonadIO m) => Handle -> [b] -> m ()

writeBed :: (BEDConvert b, MonadIO m) => FilePath -> ConduitT b o m ()

writeBed' :: (BEDConvert b, MonadIO m) => FilePath -> [b] -> m ()

Utilities

fetchSeq :: (BioSeq DNA a, MonadIO m) => Genome -> ConduitT BED (Either String (DNA a)) m ()

retreive sequences

fetchSeq' :: (BioSeq DNA a, MonadIO m) => Genome -> [BED] -> m [Either String (DNA a)]

motifScan :: (BEDLike b, MonadIO m) => Genome -> [Motif] -> Bkgd -> Double -> ConduitT b BED m ()

Identify motif binding sites

getMotifScore :: MonadIO m => Genome -> [Motif] -> Bkgd -> ConduitT BED BED m ()

Retrieve motif matching scores

getMotifPValue

Arguments

:: Monad m

=> Maybe Double

whether to truncate the motif score CDF. Doing this will significantly reduce memory usage without sacrifice accuracy.

-> [Motif]

-> Bkgd

-> ConduitT BED BED m ()

compareBed :: (BEDLike b1, BEDLike b2) => b1 -> b2 -> Ordering

Compare bed records using only the chromosome, start and end positions. Unlike the `compare' from the Ord type class, this function can compare different types of BED data types.