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

[fungazid]

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)



 
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