[Bioperl-l] HSP brain rot...

[James Wasmuth]

Hi all,

I'm using Bio::SearchIO and having problems determining which sequence I 
want to use the methods on.  The documentation states 'hit' & 'query' 
but if I use these I one of hit or query displayed, if I type nothing 
then I get the default...  

my $in = new Bio::SearchIO(-format => 'blast',
                           -file   => "$infile");

while( my $result = $in->next_result ) {
    my $query = $result->query_name;
    print "\n\nQueried sequence: $query\n";

    while( my $hit = $result->next_hit ) {
            while( my $hsp = $hit->next_hsp ) {
                print $hsp->start('hit'),"\t", $hsp->end('hit') ,"\n";
                ...

could someone cure my Tuesday afternoon blues...  :o)

many thanks...

James