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Bio::Tools::Run::Alignment::StandAloneFasta.3pm

NAME

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

SYNOPSIS

   #!/usr/bin/perl
   use Bio::Tools::Run::Alignment::StandAloneFasta;
   use Bio::SeqIO;
   use strict;
   my @arg=(
   'b' =>'15',
   'O' =>'resultfile',
   'H'=>'',
   'program'=>'fasta34'
   );
 
   my $factory=Bio::Tools::Run::Alignment::StandAloneFasta->new(@arg);
   $factory->ktup(1);
 
   $factory->library('p');
 
   #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]);
 
 

DESCRIPTION

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 ftp://ftp.virginia.edu/pub/fasta

FEEDBACK

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 of the Bioperl mailing lists. Your participation is much appreciated.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Tiequan Zhang

        Adapted for bioperl by Shawn Hoon
        Enhanced by Jason Stajich
 
 

Email tqzhang1973@yahoo.com
      shawnh@fugu-sg.org
      jason-at-bioperl.org

Appendix

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

program_name

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

executable

  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
 
 

program_dir

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

run

  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
 
 

library

  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
 
 

output

  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)
 
 

ktup

  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
 
 

_setinput

  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
 
 

_exist

  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
 
 

_setparams

  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