[Bioperl-l] error message: can't call method "next_hit" on and undefined value
Mgavi Brathwaite
lsbrath at gmail.com
Tue Jun 16 15:42:37 UTC 2009
Hello,
My method produces an error message stating that it can't call a "next_hit"
method on an undefined value.
Hello,
My method produces an error message stating that it can't call a "next_hit"
method on an undefined value.
sub hu_bl2seq_parser{
my ($maid, $maid_dir) = @_;
# Get the report
my $in = new Bio::SearchIO(-format => 'blast',
-file => ">".$maid_dir."\\".$maid."aln_hu.aln",
-report_type => 'blastn');
#open(my $out, ">$maid_dir/".$maid."aln_hu_parsed.out");
#my $out = Bio::AlignIO->newFh(-format => 'clustalw' );
my $result=$in->next_result;
my($hu_aln,$hu_mismatches);
# Get info about the first hit
my $hit = $result->next_hit;
my $name = $hit->name;
# get info about the first hsp of the first hit
my $hsp = $hit->next_hsp;
# get the alignment object
my $aln = $hsp->get_aln;
#my $percent_id = $hsp->percent_identity;
#my $aln_length = $hsp->length('total');
my @mismatches = $hsp->seq_inds('query','nomatch');
my $aln_str="";
# access the alignment string
my $strIO=IO::String->new($aln_str);
# write the string alignio in clustalw format
my $alnio = Bio::AlignIO->new(-format => 'clustalw', -fh=>$strIO);
# now the actual alignment string is accessable for printing or in
this case moving to a db table
$alnio->write_aln($aln);
$hu_aln=$aln_str;
$hu_mismatches = scalar @mismatches;
return($hu_aln, $hu_mismatches);
}
The problem is at "my $hit = $result->next_hit;"
Any help will be appreciated.
LomSpace
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