[EMBOSS] seqret segfault (refseq protein sequence, indexed with dbxflat)

[Peter Rice]

Dear Jan,

> I've run into a weird problem with seqret after downloading the complete
> protein refseq database and indexing that with dbxflat. The problem
> seems to be triggered by a rare condition, so far I've only encountered
> it with accession ZP_10312765:
> 
>     % seqret -feature -outseq=stdout -osformat=swiss ptest:ZP_10312765
> 
> Monitoring the seqret process using top, I noticed that the process
> grows to a size of 2g before segfaulting.
> 
> Trying the same with ZP_10312766, the next record in the file, causes
> no problem. Also, -osformat=fasta and -osformat=genbank work with
> ZP_10312765, so the problem seems to be with outputting the swiss format.

I can reproduce the problem with the latest EMBOSS. The problem seems to be trying to wrap a feature line to 41 bytes per record when the coded_by location is longer than the available width.
 
I will work on a patch for the latest release and also for the 6.4 release you were using.
 
Many thanks for finding this one.
 
Peter Rice
EMBOSS Team