[Bioperl-l] Exceptions thrown when parsing embl format
Rob Ewing
ewing@genome.stanford.edu
Wed, 20 Dec 2000 12:11:17 -0800 (PST)
Hi,
When parsing embl format sequence entries, I run into problems due to
slight 'errors' in the embl format.
for example , I get the following error message:
-------------------- EXCEPTION --------------------
MSG: Weird location line [1280..(1547.1700)] in reading GenBank
CONTEXT: Error in uNKNOWN CONTEXT
SCRIPT: e
STACK:
Bio::SeqIO::FTHelper::_generic_seqfeature(160)
Bio::SeqIO::embl::next_seq(296)
main::-e(1)
---------------------------------------------------
when parsing an embl format entry that has the line :
FT exon 1280..(1547.1700)
(I assume that the parser cannot figure out the start and end of this
exon feature).
How can I deal with this - is there any way to prevent an exception
being thrown and just move on to the next entry in the file. Or should
I look at ways of excluding the 'bad' entries from the file?
(All I want to do is convert a large embl format file to fasta format!)
thanks
Rob.