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

Stefan Kirov skirov at utk.edu
Tue Mar 15 08:51:02 EST 2005

Your first problem is that you cannot access SeqFeature methods 
(Annotation as well) as LargePrimarySeq inherits (unlike LargeSeq) only 
from PrimarySeq. Therefore you don't have these methods available. Two 
approaches: create an empty Seq object to hold the annotation, or read 
the file into a new LargeSeq object:
my $id=<>;
while (<>) {
I don't know what the performance will be with the second object when 
you add features. First one is far safer I think.
Next problem performance screening the sequence. Unless you have 
something BIG it is likely you will have to split the sequence in at 
least several chunks (then you can see if this disrupted a signal, 
site..etc.) or get few gigs more for your RAM (best would be some shared 
memory and a grid if you want to kill a fly with a tank :-) ).
Let me know if you have further questions.
Hope this helps and good luck.

iluminati at earthlink.net wrote:

> 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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