[Biojava-l] problem parsing genbank files

Claude Pasquier claude.pasquier at unice.fr
Fri Oct 24 06:54:34 EDT 2003


I have a problem during the parsing of some genbank file concerning the 
handling of 'LOCUS' annotation.

The line below, for example, found in the Caenorhabditis_briggsae.0.dat file 
(downloaded from ensembl site) is not correctly read by the parser :

LOCUS       ENS:cb25.fpc3857.1015654-1035120 19467 bp DNA HTG 24-MAR-2003

returns "ENS:cb25.f"

It seems that the problem has something to do with the length of the line :
- when I add a character, this raises an exception "line too short" ?!
- if I delete a char, it's OK !

Thanks for your help,

Claude Pasquier
CNRS UMR 6543. Institute of Signaling, Developmental Biology and Cancer
Centre de Biochimie, Faculté des Sciences,  06108 Nice cedex 2
Tel: +33 4 92 07 69 47

More information about the Biojava-l mailing list