Bio-Phylo

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lib/Bio/Phylo/Matrices/MatrixRole.pm  view on Meta::CPAN

sub maxname_length { $logger->warn }

sub no_residues { $logger->warn }

sub no_sequences {
    my $self = shift;
    return scalar @{ $self->get_entities };
}

sub percentage_identity { $logger->warn }

# from simplealign
sub average_percentage_identity{
   my ($self,@args) = @_;

   my @alphabet = ('A','B','C','D','E','F','G','H','I','J','K','L','M',
                   'N','O','P','Q','R','S','T','U','V','W','X','Y','Z');

   my ($len, $total, $subtotal, $divisor, $subdivisor, @seqs, @countHashes);

   if (! $self->is_flush()) {
       throw 'Generic' => "All sequences in the alignment must be the same length";
   }

lib/Bio/Phylo/Matrices/MatrixRole.pm  view on Meta::CPAN

       foreach my $res (keys %hash) {
	   $total += $hash{$res}*($hash{$res} - 1);
	   $subdivisor += $hash{$res};
       }
       $divisor += $subdivisor * ($subdivisor - 1);
   }
   return $divisor > 0 ? ($total / $divisor )*100.0 : 0;
}

# from simplealign
sub overall_percentage_identity{
   my ($self, $length_measure) = @_;

   my @alphabet = ('A','B','C','D','E','F','G','H','I','J','K','L','M',
                   'N','O','P','Q','R','S','T','U','V','W','X','Y','Z');

   my ($len, $total, @seqs, @countHashes);

   my %enum = map {$_ => 1} qw (align short long);

   throw 'Generic' => "Unknown argument [$length_measure]"

lib/Bio/Phylo/Unparsers/Figtree.pm  view on Meta::CPAN

	# fetch Meta objects, filter out the ones that are _NS_FIGTREE_,
	# turn them into a hash without the fig prefix	
	my @meta = @{ $node->get_meta };
	my %meta = map { $_->get_predicate_local => $_->get_object }
	          grep { $_->get_predicate_namespace eq $ns } @meta;
	$log->debug( Dumper(\%meta) );
	
	# there can be separate annotations that are _min and _max for
	# the same variable name stem. We combine these into a range
	# between curly braces. Also add % percentage symbol for 95%
	# HPD ranges - the % symbol is disallowed in CURIEs, hence we
	# have to bring it back here.
	my %merged;
	KEY: for my $key ( keys %meta ) {
		if ( $key =~ /^(.+?)_min$/ ) {
			my $stem = $1;
			my $max_key = $stem . '_max';
			$stem =~ s/95/95%/;
			$merged{$stem} = '{'.$meta{$key}.','.$meta{$max_key}.'}';
		}

t/24-bioperl-alignio.t  view on Meta::CPAN

    '-format'  => 'emboss',
    '-file'    => test_input_file('cysprot.water'),
    '-verbose' => -1,
);
$aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl( $str->next_aln() );
isa_ok( $aln, 'Bio::Align::AlignI' );
is( $aln->score,                      '501.50' );
is( $aln->get_seq_by_pos(1)->get_nse, 'PAPA_CARPA/3-342' );
is( $aln->get_seq_by_pos(2)->get_nse, 'CATL_HUMAN/1-331' );
SKIP: {
    skip 'percentage identity', 2, if 1;
    is( sprintf( "%.1f", $aln->overall_percentage_identity ), 33.8 );
    is( sprintf( "%.1f", $aln->average_percentage_identity ), 40.1 );
}
is( $aln->get_seq_by_pos(1)->start, 3 );
SKIP: {
    skip 'length', 1, if 1;
    is( $aln->length, 364 );
}

# EMBOSS needle
$str = Bio::AlignIO->new(
    '-format'  => 'emboss',

t/24-bioperl-alignio.t  view on Meta::CPAN

# EMBOSS water 2.2.x sparse needle
$str = Bio::AlignIO->new(
    -verbose   => $DEBUG,
    '-format'  => 'emboss',
    '-file'    => test_input_file('sparsealn.needle'),
    '-verbose' => -1,
);
$aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl( $str->next_aln() );
isa_ok( $aln, 'Bio::Align::AlignI' );
is( $aln->score, '18.0' );
is( sprintf( "%.1f", $aln->overall_percentage_identity ), 2.1 );
is( sprintf( "%.1f", $aln->average_percentage_identity ), 38.5 );
is( $aln->get_seq_by_pos(1)->length,  238 );
is( $aln->length,                     238 );
is( $aln->get_seq_by_pos(1)->get_nse, 'KV1K_HUMAN/1-108' );
is( $aln->get_seq_by_pos(2)->get_nse, 'IF1Y_HUMAN/1-143' );
is( $aln->get_seq_by_pos(1)->seq(),
        'DIQMTQSPSTLSVSVGDRVTITCEASQTVLSYLNWYQQK'
      . 'PGKAPKLLIYAASSLETGVPSRFSGQGSGTBFTFTISSVZPZBFATYYCQZYLDLPRTFGQGTKVDLKR'
      . '-' x 130 );
is( $aln->get_seq_by_pos(2)->seq(),
        ( '-' x 94 )