[Bioperl-l] getting top blast hit

[Paulo Almeida]

Nandita,

Try making this change:

print "\n", $result->query_name, "\t";
if ( my $top_hit = $result->next_hit ) { # this line changed
print $top_hit->name, "\t";
print $top_hit->significance,. "\n";
} else { # this else is optional, in case you want to report no hits
print "No hits\n";


The problem is $top_hit->name assumes there was a hit. You didn't have 
that problem before because the while() loop was checking if there was a 
hit. Now the if() does that.

-Paulo Almeida

Nandita Mullapudi wrote:

> Thanks, Sean,
> I tried the suggestion below in my script, which starts with a loop to 
> read through a list of files..
> however, now, my script stops parsing as soon as it reaches a file 
> with no hits in it.
>
> this is the error message:
>
> can't call method "name" on an undefined value at 
> /home/nandita/parse_blast-onlytophit.pl line 26, <GEN123> line 65.
>
> I realise I am not looping through completely or...
> Any suggestions?
> thanks,
> -Nandita
>
> use strict;
> use Bio::SearchIO;
> use Bio::SimpleAlign;
> my (@list, $filename);
> my $files= "/scratch/nandita/list";
> open (FH,"$files") or die "cannot create list :$!";
> while (<FH>) {
> push (@list, $_);
> # print " $_\n"; }
>
> foreach (@list) {
> $filename=$_;
> # print "$filename\n";
> my $in = new Bio::SearchIO(-format => 'blast',
> -file => "$filename");
>
> while( my $result = $in->next_result ) {
> print "\n", $result->query_name, "\t";
> my $top_hit = $result->next_hit ; {
> print $top_hit->name, "\t";
> print $top_hit->significance,. "\n";
> }}}