[Bioperl-l] BLASTing BioSeq objects
Tue, 10 Dec 2002 15:40:54 +0000
I'm trying to blast a sequence which is introduced to the program as a
string all implemented as a CGI userinterface. The sequence is in fasta
format, though I hope to extend this to any.
I thought I had been able to create a Bio::Seq object from the string,
which StandAloneBlast requires, by doing...
my $stringfh = new IO::String($query_str);
my $bioSeq_obj = new Bio::Seq(-fh => $stringfh, -format => 'fasta');
however a check on the length of the sequence in the object reveals it
to be zero in length.
Anyone any ideas? Should I first create a SeqIO object and convert this
to a Bio::Seq object and then BLAST. If so, how is this conversion done?
I'm sure the answers are in the archive but have been unable to locate