bio-0.4.6: A bioinformatics library Source code Contents Index

Bio.Alignment.BED

Description

Model the BED format, according to the spec at http:genome.ucsc.eduFAQFAQformat#format1

Synopsis

data BED = BED { chrom :: ByteString chromStart :: Offset chromEnd :: Offset name :: ByteString score :: Int strand :: Dir thickStart :: Offset thickEnd :: Offset itemRGB :: (Word8, Word8, Word8) blockSizeStart :: [(Offset, Offset)] } data Dir = Fwd | Rev readBED :: FilePath -> IO [BED] writeBED :: FilePath -> [BED] -> IO ()

Documentation

data BED Source

The BED data type Note that the specification allows a variable number of fields, with only the three first required. This definition requires all fields to be present. Constructors BED chrom :: ByteString chromStart :: Offset chromEnd :: Offset name :: ByteString score :: Int Range 0..1000 strand :: Dir thickStart :: Offset thickEnd :: Offset itemRGB :: (Word8, Word8, Word8) Available BED files appear to not support this format. RGB is therefore ignored (read and written as '0') blockSizeStart :: [(Offset, Offset)] Lists of lenght blockCount, blockStarts are relative to chromStart Instances Show BED

data Dir Source

Yet another direction data structure. Constructors Fwd Rev Instances Eq Dir Read Dir Show Dir

readBED :: FilePath -> IO [BED] Source

writeBED :: FilePath -> [BED] -> IO () Source

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