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

[Brian Osborne]

fungazid,

What version of BioPerl are you using?

If I'm not mistaken this problem has been seen before, and is now  
fixed in Bioperl 1.6.

Brian O.


On May 15, 2009, at 9:17 AM, fungazid wrote:

>
> 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-tp23559474p23559474.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
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