Bio.SeqLoc.Bed
Description
Utilities for reading and writing BED format gene annotations
- readBedTranscripts :: FilePath -> IO [Transcript]
- bedZP :: Parser Transcript
- bedTranscriptEnum :: Monad m => Iteratee [Transcript] m a -> Iteratee ByteString m a
- transcriptToBed :: ByteString -> ByteString -> Transcript -> ByteString
- transcriptToBedStd :: Transcript -> ByteString
Documentation
readBedTranscripts :: FilePath -> IO [Transcript]Source
Read all BED format annotations in a BED file
bedZP :: Parser TranscriptSource
Minimalistic Parser-style parser for a BED format line, not
including the trailing newline.
bedTranscriptEnum :: Monad m => Iteratee [Transcript] m a -> Iteratee ByteString m aSource
Iteratee to convert an Iteratee over a ByteString,
such as the standard fileDriver, into an iteratee over a
list of Transcript annotations from the file.
Arguments
| :: ByteString | score |
| -> ByteString | itemRGB |
| -> Transcript | transcript |
| -> ByteString |
Convert a Transcript to a BED annotation line, specifying the
score and itemRGB fields.
transcriptToBedStd :: Transcript -> ByteStringSource
Convert a Transcript to a BED annotation line.