Hi
I'm trying to use ensembl java API to extract info on five Prime UTR, exons,
introns,threePrimeUTR for transcripts corresponding to particular
NM_xxxxx ref seq .
Unfortunetly it looks like I incorrectly use API to get intron info.
The following is the type of the code I try to use to get intron info.
----------------------------
int exon1EndOffsetRelativeToGeneStart =
((Exon)transcript.getExons().get(0)).getLocation().getEnd() -
gene.getLocation().getStart();
int exon2StartOffsetRelativeToGeneStart =
((Exon)transcript.getExons().get(1)).getLocation().getStart() -
gene.getLocation().getStart();
String intron1 =
gene.getSequence().getString().substring(exon1EndOffsetRelativeToGeneStart
+ 1, exon2StartOffsetRelativeToGeneStart ));
------------------------------
This code would works for "ENST00000275493" EGFR NM_005228.3 , but
would not work for many if not vast majority of genes.
I would greatly appreciate info on correct way of getting intron info
for transcript.
Thank you
Dmitriy
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