[Bioperl-l] Can't find Carp/Heavy.pm using BPbl2seq module

Gisel, Andreas Andreas.Gisel@fmi.ch
Wed, 19 Jun 2002 14:28:17 +0200

Dear Bioperl users

I am new in the Perl/Bioperl world and run into the following problem I don't know how to solve:

I am using Bio::Tools::Run::StandAloneBlast and Bio::Tools::BPbl2seq for alignments between two DNA sequences (see below part of the script). The modules run in a loop and work fin until the 60th loop and the I get an error 'can't find Carp/Heavy.pm'. I checked and Carp/Heavy.pm it is at the place where it should be!!

What is the problem and how can I solve it??

Thousand Thanks

Andreas Gisel

my $seqio = Bio::SeqIO->new (-file => $queryin);
my $seq2 = $seqio->next_seq();

		$primer = substr($genome, $start, $long);

		my $seq1 = Bio::Seq->new (	-seq => $primer,
					-id => 'my seq');

		my $factory = Bio::Tools::Run::StandAloneBlast->new(	'prog' => 'blastn',
									'outfile' => 'bl2seq.out');
		my $bl2seq_report = $factory->bl2seq($seq1, $seq2);

		#my $report = Bio::Tools::BPbl2seq->new(-file => 'bl2seq.out');
		while(my $hsp = $bl2seq_report->next_feature)
			print	"start: $start ",
				"P value: ", $hsp->P, 
				" length: ", $hsp->length,
				" (1st seq length : ", $seq1->length, "  2nd seq length: ",$seq2->length,")",
	while ($start+$long < $que_leng);


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