BioPerl-Run

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lib/Bio/DB/SoapEUtilities/FetchAdaptor.pm  view on Meta::CPAN

 Title   : obj_class
 Usage   : $adaptor->obj_class
 Function: Returns the fully qualified BioPerl classname
           of the objects returned by next_obj()
 Returns : scalar string (class name)
 Args    : none

=cut

sub obj_class { shift->throw_not_implemented }

=head2 next_obj()

 Title   : next_obj
 Usage   : $obj = $adaptor->next_obj
 Function: Returns the next parsed BioPerl object from the 
           adaptor
 Returns : object of class obj_class()
 Args    : none

=cut

sub next_obj { shift->throw_not_implemented }

=head2 rewind()

 Title   : rewind
 Usage   : 
 Function: Rewind the adaptor's iterator
 Returns : 
 Args    : none

=cut

sub rewind { shift->throw_not_implemented }

=head2 result()

 Title   : result
 Usage   : 
 Function: contains the SoapEUtilities::Result object
 Returns : Bio::DB::SoapEUtilities::Result object
 Args    : none

=cut

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

 Title   : outfile
 Usage   : $prog->outfile($filename)
 Function: get/set the file to save output to
 Returns : outfile name if set
 Args    : newvalue (optional)

 
=cut

=head2  annot_file

 Title   : annot_file
 Usage   : $prog->annot_file($filename)
 Function: get/set the file name to write the MSA annotation to
 Returns : filename or undef
 Args    : filename (optional)

 
=cut

=head2  num_threads

 Title   : num_threads

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

                 log => 'g',
                 max_micro_indel => 'Y',
                 indel_params => 'D',
                 lambda => 'l',
                 extrapolate => 'e',
                 hmm => 'H',
                 catmap => 'c',
                 states => 'S',
                 reflect_strand => 'U',
                 require_informative => 'M',
                 not_informative => 'F');

our %SWITCHES = (quiet => 'q',
                 indels => 'I',
                 indels_only => 'J',
                 FC => 'X',
                 coding_potential => 'p',
                 ignore_missing => 'z');

# just to be explicit, args we don't support (yet) or we handle ourselves
our %UNSUPPORTED = (estimate_trees => 'T',

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

    view|uncompressed
    view|add_header
    view|only_header
    view|sam_input
    srt|sort_by_names
    mrg|sort_by_names
    pup|qual_last_col
    pup|sam_input
    pup|indels_only
    pup|call_cons
    pup|genot_L
    fmd|match_with_eq
);

our %param_translation = (
    'view|tab_delim' => 't',
    'view|out_file' => 'o',
    'view|pass_flags' => 'f',
    'view|refseq'   => 'T',
    'view|filt_flags' => 'F',
    'view|qual_threshold' => 'q',

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

    'pup|ref_list' => 't',
    'pup|site_list' => 'l',
    'pup|theta' => 'T',
    'pup|n_haplos' => 'N',
    'pup|exp_hap_diff' => 'f',
    'pup|indel_prob' => 'I',
    'pup|qual_last_col' => 's',
    'pup|sam_input' => 'S',
    'pup|indels_only' => 'i',
    'pup|call_cons' => 'c',
    'pup|genot_L' => 'g',
    'fmd|match_with_eq' => 'e'
    );

#
# the order in the arrayrefs is the order required
# on the command line
#
# the strings in the arrayrefs (less special chars)
# become the keys for named parameters to run_maq
#

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

            my @list2=split(" ",$orig_desc);
            my @lcs=Algorithm::Diff::LCS(\@list1,\@list2);
            my $lcs=join(" ",@lcs);

            if ($lcs eq $candidate_consensus ||
                index($orig_desc,$candidate_consensus) != -1 # addition;
                # many good (single word) annotations fall out otherwise
               ) {
                $lcs_count++;

                # Following is occurs frequently, as LCS is _not_ the longest
                # common substring ... so we can't use the shortcut either

                # if ( index($orig_desc,$candidate_consensus) == -1 ) {
                #   warn "lcs:'$lcs' eq cons:'$candidate_consensus' and
                # orig:'$orig_desc', but index == -1\n"
                # }
            }
          }
          my $perc_with_desc=(($lcs_count/$total_members))*100;
          my $perc=($lcs_count/$total_members)*100;

t/MSAProbs.t  view on Meta::CPAN

	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 = $guesser->guess;
	is($type, 'clustalw', "Expected output is clustalw formatted");
	$inputfilename = test_input_file("cysprot1a.fa");
	$aln = $factory->align($inputfilename);

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

    
    $self->_set_from_args(\@args, -methods => [@params, @switches],
                                  -create => 1);
    
    return $self;
};
my $new = *Bio::Tools::Run::WrapperBase::new; # just to avoid warning
my $obj = Bio::Tools::Run::WrapperBase->new(-test_2 => 2, -test3 => 1, -test_4 => 0);
isa_ok($obj, 'Bio::Tools::Run::WrapperBase');

# it is interface-like with throw_not_implemented methods; check their
# existance
foreach my $method (qw(run program_dir program_name version)) {
    ok $obj->can($method), "$method() exists";
}

## most methods are defined; check their function

# simple get/setters
foreach my $method (qw(error_string arguments no_param_checks save_tempfiles
                       outfile_name quiet)) {