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 listsSupport
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 StajichEmail 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 : Noneexecutable
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 foundprogram_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 sequenceslibrary
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 againstoutput
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