Module genepredext

Convert from/to GenePredExt

The GenePred(ext) format is described by UCSC

Schema for NCBI RefSeq - RefSeq genes from NCBI

Column	Type	Example	Description
name	str	NR_046018.2	Name of gene (usually transcript_id from GTF)
chrom	str	chr1	Reference sequence chromosome or scaffold
strand	enum(“+”, “-”)	+	+ or - for strand
txStart	int	11873	Transcription start position (or end position for minus strand item)
txEnd	int	14409	Transcription end position (or start position for minus strand item)
cdsStart	int	14409	Coding region start (or end position for minus strand item)
cdsEnd	int	4409	Coding region end (or start position for minus strand item)
exonCount	int	3	Number of exons
exonStarts	List of int	1873,12612,13220,	Exon start positions (or end positions for minus strand item) (with trailing comma)
exonEnds	List of int	12227,12721,14409,	Exon end positions (or start positions for minus strand item) (with trailing comma)
score	int	0	The score field indicates a degree of confidence in the feature’s existence and coordinates
name2	str	DDX11L1	Alternate name (e.g. gene_id from GTF)
cdsStartStat	enum(“none”, “unk”, “incmpl”, “cmpl”)	compl	Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat	enum(“none”, “unk”, “incmpl”, “cmpl”)	compl	Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames	List of enum(-1, 0, 1, 2)	-1,0,2,1	Exon frame {0,1,2}, or -1 if no frame for exon

The format is almost identical to RefGene, it’s only missing the bin column. So, instead of reinventing the wheel, we copied most of refgene Reader and Writer code and just added/removed the bin column.

Structs

Reader

Parses GenePredExt data and creates Transcripts.

Writer

Writes Transcripts into a BufWriter