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

[Guojun Yang]

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;
	    }