Utilities for reading and writing GTF format gene annotations
- readGtfTranscripts :: FilePath -> IO [Transcript]
- readGtfTranscriptsErr :: FilePath -> IO ([Transcript], [String])
- transcriptToGtf :: ByteString -> Transcript -> ByteString
Documentation
readGtfTranscripts :: FilePath -> IO [Transcript]Source
Read a GTF annotation file. The entire file is read at once,
because a single annotated transcript can span many lines in a GTF
file that are not required to occur in any specific order. The
transcript SpliceSeqLoc
transcript location is assembled from
exon
annotations and any CDS location is then produced from CDS
annotations, with an error occurring if the CDS is not a single
contiguous location within the transcript.
readGtfTranscriptsErr :: FilePath -> IO ([Transcript], [String])Source
transcriptToGtf :: ByteString -> Transcript -> ByteStringSource
Convert a Transcript
to a string consisting of GTF lines. These
lines will contain exon
lines for the transcript, as well as
CDS
lines if the Transcript
has a cds
.