[Bioperl-l] Strange problem with Bio::Seq::LargePrimarySeq]

[iluminati at earthlink.net]

Thanks for asking the questions!  In hindsight, I realized that I 
glossed over the problem in my frustration. 

Anyway, here's the drill.  I created a seq object from a 
chromosome-sized fasta file like so...

my $seqio = new Bio::SeqIO('-format'=>'largefasta',
                            '-file'  =>Bio::Root::IO->catfile("/Thesis 
Stuff/Chr$Chromosome/chr$Chromosome.fa"));
   
    #Create the seq object
    my $seq = $seqio->next_seq();

 From there, I want to manipulate the sequence and use the functions 
generally available to a seq object.  Now, in order to the build the seq 
object, I have to use the Bio::Seq::largefasta module.  The reason I 
need the Bio::Seq::LargePrimarySeq module is so that I can manipulate 
the sequence and get to the necessary functions.  However, I get this 
error running the script despite including the 
Bio::Seq:::LargePrimarySeq module:

Can't locate object method "add_SeqFeature" via package 
"Bio::Seq::LargePrimaryS
eq" (perhaps you forgot to load "Bio::Seq::LargePrimarySeq"?) at 
ThesisFrontEndS
cript.pl line 94, <GeneExpressionData> line 33294.


I can send you the code in question if you want to get a better look-see. 

Now, the reason I need the whole sequence is two-fold.  For one, I need 
to be able to calculate CG% of genes as an experimental control of my 
project.  The other part is that I need to be able to scan the genome 
for polyA sites with respect to their orientation to L1 sites, and 
there's no simple way to do that other than flat-out scanning the code.  
I'll definitely look into tweaking the /$tmp directory if that helps, 
but other than that, I have to at least try and make it work.

Stefan Kirov wrote:

> First you have to answer few questions: how do you get the object?/
> use Bio::Seq::LargePrimarySeq does not create an object it merely 
> makes the code available.
> /If you post you code here it will be much easier to answer your 
> questions. How do you access the sequence (I hope you have read the 
> documentation, which states that it is not generally a good idea to 
> call $seq->seq).
> How big is you /tmp? What are trying to accomplish and why you need 
> the whole seq in memory?
> Stefan
>
> I've had the same issue... I ended up breaking down the sequences into
> manageable fragments but would really like to get the largePrimarySeq
> working.  When I tried loading a chrom size sequence I just sat back
> and watched my RAM get used up (2 gigs), then the swap, then the
> crash....  So if anyone can help it'd benefit both of us!
>
> Thanks for any help,
> Garrett
>
>
> On Mon, 14 Mar 2005 16:22:40 -0500, iluminati at earthlink.net 
> <http://portal.open-bio.org/mailman/listinfo/bioperl-l>
> <iluminati at earthlink.net 
> <http://portal.open-bio.org/mailman/listinfo/bioperl-l>> wrote:
>
>> / I'm having this unuusal problem with loading this particular 
>> module.  I
>
> />/ need b/c I'm working with chromosome-sized sequence files as a 
> part of
> />/ my project, but yet it seems to not want to load properly even 
> when it's
> />/ loaded using the following statement:
> />/ />/ use Bio::Seq::LargePrimarySeq;
> />/ />/ I checked my modules, and the necessary module is there.  It 
> seems to
> />/ just not want to load.  Can anyone be of service?
> />/ />/ _______________________________________________
> />/ Bioperl-l mailing list
> />/ Bioperl-l at portal.open-bio.org 
> <http://portal.open-bio.org/mailman/listinfo/bioperl-l>
> />/ http://portal.open-bio.org/mailman/listinfo/bioperl-l
> />
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