BioPerl-Run

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lib/Bio/Tools/Run/Alignment/MSAProbs.pm  view on Meta::CPAN

 Title   : consistency
 Usage   : $prog->consistency($passes)
 Function: get/set the number of consistency transformation passes
 Returns : integer
 Args    : integer 0..5, [default 2] (optional)

 
=cut

=head2  iterations

 Title   : iterations
 Usage   : $prog->iterations($passes)
 Function: get/set the number of iterative-refinement passes
 Returns : integer
 Args    : integer 0..1000, [default 10] (optional)

 
=cut

=head2  alignment_order

 Title   : alignment_order

lib/Bio/Tools/Run/BlastPlus/Config.pm  view on Meta::CPAN

psi|best_hit_score_edge
psi|window_size
psi|query_loc
psi|outfmt
psi|num_descriptions
psi|num_alignments
psi|max_target_seqs
psi|num_threads
psi|comp_based_stats
psi|gap_trigger
psi|num_iterations
psi|out_pssm
psi|out_ascii_pssm
psi|in_msa
psi|in_pssm
psi|pseudocount
psi|inclusion_ethresh
psi|phi_pattern
rpst|import_search_strategy
rpst|export_search_strategy
rpst|db

lib/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm  view on Meta::CPAN

  Description  : (optional)

                 This enables you to tell the program to use a random
                 number generator to choose the input order of
                 species.  seed: an integer between 1 and 32767 and of
                 the form 4n+1 which means that it must give a
                 remainder of 1 when divided by 4.  Each different
                 seed leads to a different sequence of addition of
                 species.  By simply changing the random number seed
                 and re-running programs one can look for other, and
                 better trees.  iterations:

  Usage        : @params = ('jumble'=>'17); where 17 is the random seed
                 Defaults to no jumble

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one

lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm  view on Meta::CPAN

                  values are integers specifying which species to use.
                  Defaults to 1

=head2 JUMBLE

Title		: JUMBLE
Description     : (optional)
                  This enables you to tell the program to use a random
                  number generator to choose the input order of
                  species.  Input values is of the format:
                  seed,iterations eg 17,10 seed: an integer between 1
                  and 32767 and of the form 4n+1 which means that it
                  must give a remainder of 1 when divided by 4.  Each
                  different seed leads to a different sequence of
                  addition of species.  By simply changing the random
                  number seed and re-running programs one can look for
                  other, and better trees.  iterations: For a value of
                  10, this will tell the program to try ten different
                  orders of species in constructing the trees, and the
                  results printed out will reflect this entire search
                  process (that is, the best trees found among all 10
                  runs will be printed out, not the best trees from
                  each individual run).

=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/Phylo/QuickTree.pm  view on Meta::CPAN

=head2 new

 Title   : new
 Usage   : $factory = Bio::Tools::Run::Phylo::QuickTree->new(@params)
 Function: creates a new QuickTree factory
 Returns : Bio::Tools::Run::Phylo::QuickTree
 Args    : Optionally, provide any of the following (default in []):
           -upgma  => boolean # Use the UPGMA method to construct the tree [0]
           -kimura => boolean # Use the kimura translation for pairwise
                              # distances [0]
           -boot   => int     # Calculate bootstrap values with n iterations [0]

=cut

sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    
    # for consistency with other run modules, allow params to be dashless
    my %args = @args;
    while (my ($key, $val) = each %args) {

lib/Bio/Tools/Run/Phylo/QuickTree.pm  view on Meta::CPAN

        $self->{kimura} = $bool;
    }
    return $self->{kimura} || 0;
}

=head2 boot

 Title   : boot
 Usage   : $factory->boot(100);
 Function: Choose to calculate bootstrap values with the supplied number of
           iterations.
 Returns : int (default 0)
 Args    : None to get, int to set.

=cut

sub boot {
    my ($self, $int) = @_;
    if (defined ($int)) {
        $self->{boot} = $int;
    }

lib/Bio/Tools/Run/StandAloneBlast.pm  view on Meta::CPAN

 @params = (-database => 'swissprot', -outfile => 'blast1.out');
 $factory = Bio::Tools::Run::StandAloneBlast->new(@params);

 # Blast a sequence against a database:
 $str = Bio::SeqIO->new(-file=>'t/amino.fa', -format => 'Fasta');
 $input = $str->next_seq();
 $input2 = $str->next_seq();
 $blast_report = $factory->blastall($input);

 # Run an iterated Blast (psiblast) of a sequence against a database:
 $factory->j(3);    # 'j' is blast parameter for # of iterations
 $factory->outfile('psiblast1.out');
 $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
 $blast_report = $factory->blastpgp($input);

 # Use blast to align 2 sequences against each other:
 $factory = Bio::Tools::Run::StandAloneBlast->new(-outfile => 'bl2seq.out');
 $factory->bl2seq($input, $input2);

 # Experimental support for WU-Blast 2.0
 my $factory = Bio::Tools::Run::StandAloneBlast->new(-program =>"wublastp",

t/MSAProbs.t  view on Meta::CPAN

	is $aln->num_sequences, 7;
	my $s1_perid = POSIX::ceil($aln->average_percentage_identity);
	is($s1_perid == 43, 1);
	
	my $annotfile = test_output_file();
	my $outfile = test_output_file();
	# add some more params
	@params = ('-quiet'           => 1,
		       '-verbose'         => 0,
	           '-outfile'         => $outfile,
		       '-iterations'      => 5,
		       '-clustalw'        => 1,
		       '-consistency'     => 2,
		       '-alignment_order' => 1,
		       '-annot_file'      => $annotfile,
	
		   );
	$factory = Bio::Tools::Run::Alignment::MSAProbs->new(@params);
	my @methods = qw(quiet verbose outfile iterations clustalw consistency
	                 alignment_order annot_file version num_threads);
	can_ok($factory, @methods);
	is($factory->annot_file, $annotfile,'annotation file');
	$aln = $factory->align($seq_array_ref);
	is $aln->num_sequences, 7;
	$s1_perid = POSIX::ceil($aln->average_percentage_identity);
	is($s1_perid == 43, 1 );
	
	my $guesser = Bio::Tools::GuessSeqFormat->new(-file => $outfile);
	my $type = $guesser->guess;

t/Tools/Run/StandAloneBlast.t  view on Meta::CPAN

	
	# use swissprot
	my $amino_database_file = File::Spec->catfile($Bio::Tools::Run::StandAloneBlast::DATADIR, $amino_database);
	SKIP: {
		skip "Database $amino_database not found, skipping tests on it", 3 unless -e $amino_database_file;
		
		@params = ('database' => $amino_database, '-verbose' => $verbose);
		$factory = Bio::Tools::Run::StandAloneBlast->new(@params);
		
		my $iter = 2;
		$factory->j($iter);    # 'j' is blast parameter for # of iterations
		my $new_iter = $factory->j();
		is $new_iter, 2, "set blast parameter";
		
		my $blast_report = $factory->blastpgp($seq3)->next_result;
		is $blast_report->number_of_iterations, $testresults[$testcount];
		
		$factory->_READMETHOD('blast_pull');
		$iter = 2;
		$factory->j($iter);    # 'j' is blast parameter for # of iterations
		$new_iter = $factory->j();
		is $new_iter, $iter, "set blast parameter";
		
	}
}