[Bioperl-l] Strange problem with Bio::Seq::LargePrimarySeq]
iluminati at earthlink.net
iluminati at earthlink.net
Mon Mar 14 21:39:43 EST 2005
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',
#Create the seq object
my $seq = $seqio->next_seq();
From there, I want to manipulate the sequence and use the functions
generally available to a seq object. Now, in order to the build the seq
object, I have to use the Bio::Seq::largefasta module. The reason I
need the Bio::Seq::LargePrimarySeq module is so that I can manipulate
the sequence and get to the necessary functions. However, I get this
error running the script despite including the
Can't locate object method "add_SeqFeature" via package
eq" (perhaps you forgot to load "Bio::Seq::LargePrimarySeq"?) at
cript.pl line 94, <GeneExpressionData> line 33294.
I can send you the code in question if you want to get a better look-see.
Now, the reason I need the whole sequence is two-fold. For one, I need
to be able to calculate CG% of genes as an experimental control of my
project. The other part is that I need to be able to scan the genome
for polyA sites with respect to their orientation to L1 sites, and
there's no simple way to do that other than flat-out scanning the code.
I'll definitely look into tweaking the /$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?
> 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,
> On Mon, 14 Mar 2005 16:22:40 -0500, iluminati at earthlink.net
> <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?
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