[Bioperl-l] looks like a Bio::SeqIO error
Kevin Brown
Kevin.M.Brown at asu.edu
Fri May 15 16:03:16 UTC 2009
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.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
More information about the Bioperl-l
mailing list