Bio.SeqLoc.TranscriptTable

Minimal tab-delimited annotation of Transcript locations. Each Transcript has one line, containing the geneId and trxId fields, followed by the LocRepr representation of the SpliceSeqLoc location of the transcript, and then the location of the CDS within the transcript or n/a if there is no CDS.

Documentation

readTable :: FilePath -> IO [Transcript]

Read a transcript table file as a list of annotated transcripts

parseLine :: ByteString -> Maybe Transcript

Parse a transcript table line, not including the newline

writeTable :: FilePath -> [Transcript] -> IO ()

Write a transcript table file

unparseLine :: Transcript -> ByteString

Produce a single transcript table line for a Transcript, newline not included.