@groovy.util.logging.Log class RefGenes extends java.lang.Object
A convenience class that is set up to parse the UCSC RefGene database as a RangedData object. This allows querying it over ranges to find transcripts and easy access to the properties of ranges so found.
A set of utility operations are additionally available for querying other features (lookup by gene, transcript name, etc).
| Type | Name and description |
|---|---|
static java.lang.Object |
COLUMN_NAMES |
static java.lang.String |
UCSC_REFGENE_URLDefault UCSC download URL for the refgene database |
java.util.Map<java.lang.String, java.util.List<java.lang.Integer>> |
geneToTranscriptsTranscripts indexed by gene |
RangedData |
refData |
java.util.Map<java.lang.String, gngs.Region> |
transcriptIndex |
| Type Params | Return Type | Name and description |
|---|---|---|
|
static RefGenes |
download(java.lang.String genomeVersion) |
|
java.util.Map<java.lang.String, java.lang.Integer> |
getCDS(IRegion region)Compute a map of gene symbols with the amount of coding sequence overlapped by each gene for the given region |
|
Regions |
getExons(java.lang.String gene, boolean codingOnly)Return a regions object containing a region for each unique exon in the transcript. |
|
java.util.List<gngs.Region> |
getExons(IRegion region) |
|
gngs.Region |
getGeneRegion(java.lang.String hgncSymbol)Look up the entire span of a gene from its HGNC symbol |
|
java.util.List<java.lang.String> |
getGenes(IRegion region)
|
|
Regions |
getSpliceSites(java.lang.String transcript)Return a regions object containing a region for each unique exon in the transcript. |
|
Regions |
getTranscriptExons(java.lang.String transcriptId) |
|
java.util.List<java.lang.String> |
getTranscriptIds(java.lang.String gene)Return the names of all the transcripts (NM_... identifiers) for the given HGNC symbol |
|
java.util.List<gngs.Region> |
getTranscripts(java.lang.String gene)Return a list of transcript objects as Regions having all the full properties of a transcript (see COLUMN_NAMES) |
|
void |
index() |
|
void |
load(java.io.Reader r) |
| Methods inherited from class | Name |
|---|---|
class java.lang.Object |
java.lang.Object#wait(long), java.lang.Object#wait(long, int), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll() |
Default UCSC download URL for the refgene database
Transcripts indexed by gene
Compute a map of gene symbols with the amount of coding sequence overlapped by each gene for the given region
Return a regions object containing a region for each unique exon in the transcript. If two exons overlap, the union of the two is returned. @return
Look up the entire span of a gene from its HGNC symbol @return
region - the region to queryReturn a regions object containing a region for each unique exon in the transcript. If two exons overlap, the union of the two is returned. @return
Return the names of all the transcripts (NM_... identifiers) for the given HGNC symbol @return
Return a list of transcript objects as Regions having all the full properties of a transcript (see COLUMN_NAMES)
Groovy Documentation