[Biojava-l] Parsing EMBL files from Ensembl

[Stein Aerts]

Since today, apparantly something changed on the "export data" function of Ensembl. When retrieving a gene based on its ensembl id, e.g. ENSG00000110092 with 2000 bp on either side, and requesting only gene features, then until yesterday, the resulting EMBL formatted file had ID= ENSG00000110092 but now it has ID :

ID Chromosome 11 71948701 to 71966070 ENSEMBL; DNA; HUM; 17370 BP.

More importantly the parser in BioJava with EMBL format cannot parse it, it complains by telling me

This line could not be parsed: CDS join(-1151..-840,1654..1777,1995..2434)
This line could not be parsed: 12014..12175)
This line could not be parsed: CDS join(3927..4460,4728..4887,8890..9038,12014..12178)
This line could not be parsed: exon -1151..-840
This line could not be parsed: exon 1654..1777

and so on.

Would there be anyone who could help me out on this?

Thanks a lot,
Stein Aerts.




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