class Gencode extends java.lang.Object
Class implementing parsing of Gencode GFF3 format
This class passes a GFF3 file and creates a 3 level structure made up of gngs.gencode.Gene, and gngs.gencode.Exon objects, representing the core elements within the GFF3. Sub elements of these within the file are ignored.
There are two basic ways of using the class, and which one is better depends on the kind of access you expect to make.
def gencode = new Gencode()
To use indexed access, the gencode source file must be first sorted by position and then indexed using tabix. A suitable command to do that is as follows:
(zgrep ^"#" gencode.v40.basic.annotation.gff3.gz; zgrep -v ^"#" gencode.v40.basic.annotation.gff3.gz | sort -k1,1 -k4,4n) | bgzip > gencode.v40.basic.annotation.gff3.bgz tabix -p gff gencode.v40.basic.annotation.gff3.bgz
After sorting and indexing, you may load specific regions by using the loadRegion method:
Gencode gencode = new Gencode(gencode)
gencode.loadRegion(new Region('chr1:1335276-1349418'))
| Type | Name and description |
|---|---|
java.util.Map<java.lang.String, Feature> |
features |
Regions |
geneRegions |
java.util.Map<java.lang.String, gngs.gencode.Gene> |
genes |
htsjdk.tribble.index.Index |
index |
boolean |
loaded |
ProgressCounter |
progress |
java.lang.Object |
source |
java.util.List<Region> |
unresolvedEntriesAtPosition |
| Constructor and description |
|---|
Gencode
(java.lang.Object fileLike) |
| Type Params | Return Type | Name and description |
|---|---|---|
|
gngs.gencode.Gene |
getGeneRegion(java.lang.String geneSymbol) |
|
Gencode |
load() |
|
void |
loadRegion(IRegion query) |
| 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() |
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