[Bioperl-l] help on large sequence with Bio::Index::Fasta!

[Lincoln Stein]

As far as I know Bio::Index::Fasta works fine with large sequences.  
I've used it with worm chromosomes up to 20 MB.  You might try 
Bio::DB::Fasta in a pinch, since it stores the data differently.

Lincoln

On Monday 24 January 2005 02:02 pm, Guojun Yang wrote:
> Hi, everybody,
> I got another difficult situation:
> I am running a local blast and sequence retrieval. The following
> sub works OK for one of my local DB1, but not for my local DB2. DB1
> contains sequences of PACs and BACs (I believe the average size is
> ~100 or 200 kb), but DB2 contains entries of contigs as large as
> 30Mb. The error says the $seq object is undefined! I believe the
> problem is the size of the large entries in DB2. Can we use
> LargeSeq when we do retrieval? Can anybody help me on how we can
> use it with Bio::Index::Fasta?. Thank you for your comments in
> advance! Yang
>
>
>
> sub getseq {
> my $id=$_[0];
> my $file_name = $_[1];
> my $inx=Bio::Index::Fasta->new (-filename => $file_name.".idx",
>                                 -write_flag => 1);
> $inx->id_parser(\&get_id);
> $inx->make_index($file_name);
> $seq = $inx->fetch($id);
> return $seq;
> 	    }
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

NOTE: Please copy Sandra Michelsen <michelse at cshl.edu> on
all emails regarding scheduling and other time-critical topics.
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: application/pgp-signature
Size: 189 bytes
Desc: not available
Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20050125/b53329ac/attachment.bin