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://redmine.open-bio.org/projects/bioperl/

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 preceded 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