[Bioperl-l] looks like a Bio::SeqIO error

Chris Fields cjfields at illinois.edu
Fri May 15 14:42:01 EDT 2009

As mentioned in the thread by Kevin, using LargeSeq may not be the  
best route as it generates a tmpdir/tmpfile for each sequence, so you  
are probably reaching a hard limit for the number of temp files for  
your system or for File::Temp.  The oddity is one or the other (or  
both) are not removed, so I think this is a legit bug.

Regardless, there's a good reason this hasn't been encountered  
before.  If you have ~30,000 sequences that you extract subseqs from  
you should seriously consider using a flat file db such as  
Bio::DB::Fasta or similar.  It is capable of handling very large  
sequences or files and can extract subseqs easily.


On May 15, 2009, at 12:12 PM, fungazid wrote:

> After installing XML-SAX module, the my installation of bioperl 1.6  
> was
> successful (I didn't need to force install).But the error I reported
> previously (Too many links at /usr/local/share/perl/5.8.8/Bio/Root/ 
> IO.pm
> line 740) still exists.
> -- 
> View this message in context: http://www.nabble.com/looks-like-a-Bio%3A%3ASeqIO-error-tp23559474p23563950.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
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