Provided by: libbio-perl-run-perl_1.6.9-2_all bug


       Bio::Tools::Run::Alignment::StandAloneFasta - Object for the local execution of the Fasta3
       programs ((t)fasta3, (t)fastx3, (t)fasty3 ssearch3)


         use Bio::Tools::Run::Alignment::StandAloneFasta;
         use Bio::SeqIO;
         use strict;
         my @arg=(
         'b' =>'15',
         'O' =>'resultfile',

         my $factory=Bio::Tools::Run::Alignment::StandAloneFasta->new(@arg);


         #print result file name
         print $factory->O;

         my @fastreport=$factory->run($ARGV[0]);

         foreach  (@fastreport) {
               print "Parsed fasta report:\n";
           my $result = $_->next_result;
           while( my $hit = $result->next_hit()) {
              print "\thit name: ", $hit->name(), "\n";
                while( my $hsp = $hit->next_hsp()) {
                print "E: ", $hsp->evalue(), "frac_identical: ",
               $hsp->frac_identical(), "\n";

          #pass in seq objects
          my $sio = Bio::SeqIO->new(-file=>$ARGV[0],-format=>"fasta");
          my $seq = $sio->next_seq;
          my @fastreport=$factory->run($ARGV[0]);


       This wrapper works with version 3 of the FASTA program package (see W. R. Pearson and D.
       J. Lipman (1988), "Improved Tools for Biological Sequence Analysis", PNAS 85:2444-2448
       (Pearson and Lipman, 1988); W. R.  Pearson (1996) "Effective protein sequence comparison"
       Meth. Enzymol.  266:227-258 (Pearson, 1996); Pearson et. al. (1997) Genomics 46:24-36
       (Zhang et al., 1997); Pearson, (1999) Meth. in Molecular Biology 132:185-219 (Pearson,
       1999).  Version 3 of the FASTA packages contains many programs for searching DNA and
       protein databases and one program (prss3) for evaluating statistical significance from
       randomly shuffled sequences.

       Fasta is available at


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AUTHOR - Tiequan Zhang

              Adapted for bioperl by Shawn Hoon
              Enhanced by Jason Stajich



       The rest of the documendation details each of the object methods. Internal methods are
       preceded with a underscore

        Title   : program_name
        Usage   : $factory->program_name()
        Function: holds the program name
        Returns:  string
        Args    : None

        Title   : executable
        Usage   : my $exe = $blastfactory->executable('blastall');
        Function: Finds the full path to the 'codeml' executable
        Returns : string representing the full path to the exe
        Args    : [optional] name of executable to set path to
                  [optional] boolean flag whether or not warn when exe is not found

        Title   : program_dir
        Usage   : $factory->program_dir(@params)
        Function: returns the program directory, obtained from ENV variable.
        Returns:  string
        Args    :

        Title   : run

        Usage   : my @fasta_object = $factory->($input,$onefile);
                  where $factory is the name of executable FASTA program;
                  $input is file name containing the sequences in the format
                  of fasta  or Bio::Seq object or array of Bio::Seq object;
                  $onefile is 0 if you want to save the outputs to different files
                  default: outputs are saved in one file

        Function: Attempts to run an executable FASTA program
                  and return array of  fasta objects containing the fasta report
        Returns : aray of fasta report object
                  If the user specify the output file(s),
                  the raw fasta report will be saved
        Args    : sequence object OR array reference of sequence objects
                  filename of file containing fasta formatted sequences

        Title   : library
        Usage   : my $lb = $self->library
        Function: Fetch or set the name of the library to search against
        Returns : The name of the library
        Args    : No argument if user wants to fetch the name of library file;
                  A letter or a string of letter preceded by %;
                  (e.g. P or %pn, the letter is  the character in the third field
                  of any line of fastlibs file  ) or the name of library file
                  (if environmental variable FASTLIBS is not set);
                   if user wants to set the name of library file to search against

        Title   : output
        Usage   : $obj->output($newval)
        Function: The output directory if we want to use this
        Example :
        Returns : value of output (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

        Title   :  ktup
        Usage   :  my $ktup = $self->ktup
        Function:  Fetch or set the ktup value for executable FASTA programs
        Example :
        Returns :  The value of ktup  if defined, else undef is returned
        Args    :  No argument if user want to fetch ktup value; A integer value between 1-6 if user want to set the
                  ktup value

        Title   :  _setinput
        Usage   :  Internal function, not to be called directly
        Function:   Create input file(s) for Blast executable
        Example :
        Returns : array of Bio::Seq object reference
        Args    : Seq object reference or input file name

        Title   : _exist
        Usage   : Internal function, not to be called directly
        Function: Determine whether a executable FASTA program can be found
                  Cf. the DESCRIPTION section of this POD for how to make sure
                  for your FASTA installation to be found. This method checks for
                  existence of the blastall executable in the path.
        Returns : 1 if FASTA program found at expected location, 0 otherwise.
        Args    :  none

        Title   :  _setparams
        Usage   :  Internal function, not to be called directly
        Function:  Create parameter inputs for FASTA executable
        Returns : part of parameter string to be passed to FASTA program
        Args    : none

perl v5.18.1                                2013-Bio::Tools::Run::Alignment::StandAloneFasta(3pm)