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

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://bio.perl.org/MailList.html - About the mailing lists

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.bioperl.org/ Adapted for bioperl by Shawn Hoon Enhanced by Jason Stajich Email tqzhang1973@yahoo.com shawnh@fugu-sg.org jason-at-bioperl.org 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, obtiained 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