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

[Kevin Brown]

How large are the individual sequences? You have more than 30,000
sequences in there? Then I wouldn't recommend using the LargeFasta
format as each of those sequences could easily be loaded and held in
memory. LargeFasta really seems to be better for holding large
individual sequences (e.g. a human chromosome).

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of fungazid
> Sent: Friday, May 15, 2009 6:18 AM
> To: Bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] looks like a Bio::SeqIO error
> 
> 
> Hello,
> 
> I hope this is the right address for bioperl programming 
> issues. Bioperl
> saves me a lot of time (not to re-invent the wheel), but 
> there are some
> extremely irritating problems (I would change the code myself 
> if I knew
> how).
> 
> I am trying to read a file (~20MB) containing multiple fasta 
> sequences:
> >a
> AGTAGTGAGTGCGCTGA.........
> >b
> GCGCTGAAGTAGTGAGT.......
> >c
> AGTAGTGAGTGCGCTGA.........
> >d...........
> 
> with the following lines:
> 
> my $seqin = Bio::SeqIO->new('-format'=>'largefasta','-file'=>$file1);
> 
> LOOP1: while ( my $seqobj1 = $seqin->next_seq())
> 
> {
> ......
> my $seq=$seqobj1->subseq(1,$seqobj1->length);
> .......
> }
> 
> 
> This works right for the first ~30000 contig sequences but then the
> following message appears:
> 
> Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory
> /tmp/6eS92VzVjm: Too many links at 
> /usr/share/perl5/Bio/Root/IO.pm line 744
> 
> What to do ??? (this is only one of some different Bioperl 
> related bugs that
> I'm experiencing)
> 
> 
> 
>  
> -- 
> View this message in context: 
> http://www.nabble.com/looks-like-a-Bio%3A%3ASeqIO-error-tp2355
> 9474p23559474.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
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