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lib/Bio/Tools/Gel.pm  view on Meta::CPAN

    use Bio::PrimarySeq;
    use Bio::Restriction::Analysis;
    use Bio::Tools::Gel;

    # get a sequence
    my $d = 'AAAAAAAAAGAATTCTTTTTTTTTTTTTTGAATTCGGGGGGGGGGGGGGGGGGGG';
    my $seq1 = Bio::Seq->new(-id=>'groundhog day',-seq=>$d);

    # cut it with an enzyme
    my $ra=Bio::Restriction::Analysis->new(-seq=>$seq1);
    @cuts = $ra->fragments('EcoRI'), 3;

    # analyse the fragments in a gel
    my $gel = Bio::Tools::Gel->new(-seq=>\@cuts,-dilate=>10);
    my %bands = $gel->bands;
    foreach my $band (sort {$b <=> $a} keys %bands){
      print $band,"\t", sprintf("%.1f", $bands{$band}),"\n";
    }

    #prints:
    #20   27.0
    #25   26.0
    #10   30.0

t/Gel.t  view on Meta::CPAN

	
    use_ok('Bio::PrimarySeq');
    use_ok('Bio::Restriction::Analysis');
    use_ok('Bio::Tools::Gel');
}

my $seq1 = Bio::PrimarySeq->new(-id=>'groundhog day',
                                -seq=>'AAAAAAAAAGAATTCTTTTTTTTTTTTTTGAATTCGGGGGGGGGGGGGGGGGGGG');

my $ra=Bio::Restriction::Analysis->new(-seq=>$seq1);
is my @cuts = $ra->fragments('EcoRI'), 3;

ok my $gel = Bio::Tools::Gel->new(-seq=>\@cuts,-dilate=>10);
ok my %bands = $gel->bands;
my @bands = (26, 27, 30);
my $c = 0;
foreach my $band (sort {$b <=> $a} keys %bands){
    #print $band,"\t",  sprintf("%.1f", $bands{$band}), "\n";
    is $bands[$c],  sprintf("%.0f", $bands{$band});
    $c++;
}