#StandAloneFasta.pm v1.00 2002/11/01
#
#Bioperl module for Bio::Tools::Run::Alignment::StandAloneFasta
#
# Written by Tiequan Zhang
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Shawn Hoon
# Copyright Tiequan Zhang
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Alignment::StandAloneFasta - Object for the local
execution of the Fasta3 programs ((t)fasta3, (t)fastx3, (t)fasty3
ssearch3)
=head1 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($ARGV[0]);
=head1 DESCRIPTION
This wrapper works with version 3 of the FASTA program package (see
W. R. Pearson and D. J. Lipman (1988), "Improved Tools for Biological
Sequence Analysis", PNAS 85:2444-2448 (Pearson and Lipman, 1988);
W. R. Pearson (1996) "Effective protein sequence comparison"
Meth. Enzymol. 266:227-258 (Pearson, 1996); Pearson et. al. (1997)
Genomics 46:24-36 (Zhang et al., 1997); Pearson, (1999) Meth. in
Molecular Biology 132:185-219 (Pearson, 1999). Version 3 of the FASTA
packages contains many programs for searching DNA and protein
databases and one program (prss3) for evaluating statistical
significance from randomly shuffled sequences.
Fasta is available at ftp://ftp.virginia.edu/pub/fasta
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Tiequan Zhang
Adapted for bioperl by Shawn Hoon
Enhanced by Jason Stajich
Email tqzhang1973@yahoo.com
shawnh@fugu-sg.org
jason-at-bioperl.org
=head1 Appendix
The rest of the documendation details each of the object
methods. Internal methods are preceded with a underscore
=cut
package Bio::Tools::Run::Alignment::StandAloneFasta;
use vars qw ($AUTOLOAD @ISA $library %parameters
$ktup @FASTA_PARAMS %OK_FIELD @OTHER_PARAMS);
use strict;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Seq;
use Bio::SeqIO;
use Bio::SearchIO;
use Bio::Tools::Run::WrapperBase;
BEGIN {
@FASTA_PARAMS=qw(a A b c E d f g h H i j l L M m n O o p Q q r R s S w x y z);
@OTHER_PARAMS =qw(program output database);
foreach my $att (@FASTA_PARAMS, @OTHER_PARAMS) {$OK_FIELD{$att}++;}
$ktup=2;
%parameters=('H' => '',
'q' => '',
'm' =>'1', 'O' =>'');
}
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
sub new {
my ($caller,@args)=@_;
#chained new
my $self = $caller->SUPER::new(@args);
while(@args){
my $attr = shift @args;
my $value = shift @args;
next if ($attr=~/^-/ || ! $attr);
$self->$attr($value);
}
return $self;
}
sub AUTOLOAD {
my $self = shift;
my $attr = $AUTOLOAD;
$attr =~ s/.*:://;
$self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
$self->{$attr} = shift if @_;
return $self->{$attr};
}
=head2 program_name
Title : program_name
Usage : $factory->program_name()
Function: holds the program name
Returns: string
Args : None
=cut
sub program_name {
my ($self) = shift;
return $self->program(@_);
}
=head2 executable
Title : executable
Usage : my $exe = $blastfactory->executable('blastall');
Function: Finds the full path to the 'codeml' executable
Returns : string representing the full path to the exe
Args : [optional] name of executable to set path to
[optional] boolean flag whether or not warn when exe is not found
=cut
sub executable {
my ($self, $exename, $exe,$warn) = @_;
$exename = 'fasta34' unless defined $exename;
if( defined $exe && -x $exe ) {
$self->{'_pathtoexe'}->{$exename} = $exe;
}
unless( defined $self->{'_pathtoexe'}->{$exename} ) {
my $f = $self->program_path($exename);
$exe = $self->{'_pathtoexe'}->{$exename} = $f if(-e $f && -x $f );
# This is how I meant to split up these conditionals --jason
# if exe is null we will execute this (handle the case where
# PROGRAMDIR pointed to something invalid)
unless( $exe ) { # we didn't find it in that last conditional
if( ($exe = $self->io->exists_exe($exename)) && -x $exe ) {
$self->{'_pathtoexe'}->{$exename} = $exe;
} else {
$self->warn("Cannot find executable for $exename") if $warn;
$self->{'_pathtoexe'}->{$exename} = undef;
}
}
}
return $self->{'_pathtoexe'}->{$exename};
}
=head2 program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
=cut
sub program_dir {
return Bio::Root::IO->catfile($ENV{FASTADIR}) if $ENV{FASTADIR};
}
=head2 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;
$onefile is 0 if you want to save the outputs to different files
default: outputs are saved in one file
Function: Attempts to run an executable FASTA program
and return array of fasta objects containing the fasta report
Returns : aray of fasta report object
If the user specify the output file(s),
the raw fasta report will be saved
Args : sequence object OR array reference of sequence objects
filename of file containing fasta formatted sequences
=cut
sub run {
my ($self,$input,$onefile)=@_;
local * FASTARUN;
$self->io->_io_cleanup;
my $program = $self->executable($self->program_name) ||
$self->throw("FASTA program not found or not executable.\n");
# You should specify a library file
$self->throw("You didn't choose library.\n") unless ( $library);
my @seqs = $self->_setinput($input);
return 0 unless (@seqs);
my @fastobj;
my ($fhout, $tempoutfile)=$self->io->tempfile(-dir=>$self->tempdir);
my $outfile=$self->O();
# The outputs from executable FASTA program will
# be saved into different files if $onefile is 0,
# else will be concatenated into one file
my $onfile = (!defined $onefile || $onefile =~ /^0$/);
unless( $onfile ) {
my $count=0;
# do some fancy stuff here to test if we are running fasta34
# with mlib so we just pass in a single file rather than
# running fasta N times
# (not implemented yet)
foreach my $seq (@seqs){
$count++;
# Decide if the output will be saved into a temporary file
if( $outfile ) {
$self->O(sprintf("%s_%d",$outfile,$count));
}
my ($fhinput,$teminputfile)=
$self->io->tempfile(-dir=>$self->tempdir);
my $temp = Bio::SeqIO->new(-fh=>$fhinput, '-format'=>'Fasta');
$temp->write_seq($seq);
$temp->close();
close $fhinput;
undef $fhinput;
my $para= $self->_setparams;
$para .=" $teminputfile $library $ktup";
$para ="$program $para";
my $object;
unless( $outfile ) {
open(FASTARUN, "$para |") || $self->throw($@);
$object = Bio::SearchIO->new(-fh=>\*FASTARUN,
-format=>"fasta");
} else {
if ( $self->verbose() < 0) {
my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';
$para .= " >$null 2>$null";
} else {
$self->debug("Going to execute: $para");
}
my $status = system($para);
$self->throw("$para crashed: $?\n" )unless ($status==0);
$object = Bio::SearchIO->new(-file=>$self->O,
-format=>"fasta");
}
push @fastobj, $object;
}
} else {
if ($outfile){
open (FILE, ">$outfile") or $self->throw("can't use $outfile:$!");
close(FILE);
}
foreach my $seq (@seqs){
my ($fhinput,$teminputfile)=$self->io->tempfile(-dir=>$self->tempdir);
my $temp=Bio::SeqIO->new(-fh=>$fhinput, '-format'=>'fasta');
$temp->write_seq($seq);
$temp->close();
close $fhinput;
undef $fhinput;
$self->O($tempoutfile) if( $outfile );
my $para= $self->_setparams;
$para .= " $teminputfile $library $ktup";
$para ="$program $para";
my $object;
unless( $outfile ) {
open(FASTARUN, "$para |") || $self->throw($@);
$object=Bio::SearchIO->new(-fh=>\*FASTARUN,
-format=>"fasta");
} else {
if ( $self->verbose() < 0) {
my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';
$para .= " >$null 2>$null";
} else {
$self->debug("Going to execute: $para");
}
my $status = system($para);
$self->throw("$para crashed: $?\n" )unless ($status==0);
$object = Bio::SearchIO->new(-file=>$self->O,
-format=>"fasta");
}
push @fastobj, $object;
# The output in the temporary file
# will be saved at the end of $outfile
if($outfile){
open (FHOUT, $tempoutfile) or die("can't open the $tempoutfile file");
open (FH, ">>$outfile") or die("can't use the $outfile file");
print FH (<FHOUT>);
close (FHOUT);
close (FH);
}
}
}
return @fastobj;
}
=head2 library
Title : library
Usage : my $lb = $self->library
Function: Fetch or set the name of the library to search against
Returns : The name of the library
Args : No argument if user wants to fetch the name of library file;
A letter or a string of letter preceded by %;
(e.g. P or %pn, the letter is the character in the third field
of any line of fastlibs file ) or the name of library file
(if environmental variable FASTLIBS is not set);
if user wants to set the name of library file to search against
=cut
sub library {
my($self,$lb)=@_;
return $library if (!defined($lb));
if ( ($lb =~ /^%[a-zA-Z]+$/)||($lb=~ /^[a-zA-Z]$/)){
if(! defined $ENV{'FASTLIBS'} ){
$self->throw("abbrv. list request but FASTLIBS undefined, cannot use $lb");
}
} else {
unless ( -e $lb){
$self->throw("cannot open $lb library");
}
}
return $library=$lb;
}
*database = \&library;
=head2 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)
=cut
sub output{
my $self = shift;
return $self->{'output'} = shift if @_;
return $self->{'output'};
}
=head2 ktup
Title : ktup
Usage : my $ktup = $self->ktup
Function: Fetch or set the ktup value for executable FASTA programs
Example :
Returns : The value of ktup if defined, else undef is returned
Args : No argument if user want to fetch ktup value; A integer value between 1-6 if user want to set the
ktup value
=cut
sub ktup {
my($self,$k)=@_;
if(!defined($k)){return $ktup;}
if ($k =~ /^[1-6]$/){
$ktup=$k;
return $ktup
} else {
$self->warn("You should set the ktup value between 1-6. The FASTA program will decide your default ktup value.");
return $ktup= undef;
}
}
=head2 _setinput
Title : _setinput
Usage : Internal function, not to be called directly
Function: Create input file(s) for Blast executable
Example :
Returns : array of Bio::Seq object reference
Args : Seq object reference or input file name
=cut
sub _setinput {
my ($self, $input) = @_;
if( ! defined $input ) {
$self->throw("Calling fasta program with no input");
}
my @seqs;
if( ! ref $input ) {
if( -e $input ) {
my $seqio = Bio::SeqIO->new(-format => 'fasta', -file => $input);
while( my $seq = $seqio->next_seq ) {
push @seqs, $seq;
}
} else {
$self->throw("Input $input was not a valid filename");
}
} elsif( ref($input) =~ /ARRAY/i ) {
foreach ( @$input ) {
if( ref($_) && $_->isa('Bio::PrimarySeqI') ) {
push @seqs, $_;
} else {
$self->warn("Trying to add a " . ref($_) ." but expected a Bio::PrimarySeqI");
}
}
if( ! @seqs) {
$self->throw("Did not pass in valid input -- no sequence objects found");
}
} elsif( $input->isa('Bio::PrimarySeqI') ) {
push @seqs, $input;
}
return @seqs;
}
=head2 _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
=cut
sub _exist {
my $exe = shift @_;
return 0 unless($exe =~ /fast|ssearch/);
$exe .='.exe' if ($^O =~ /mswin/i);
my $f;
return ($f=Bio::Root::IO->exists_exe($exe))&&(-x $f);
}
=head2 _setparams
Title : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for FASTA executable
Returns : part of parameter string to be passed to FASTA program
Args : none
=cut
sub _setparams {
my ($self,$attr,$value);
$self = shift;
my $para = "";
foreach my $attr(@FASTA_PARAMS) {
$value = $self->$attr();
next unless (defined $value);
$para .=" -$attr $value";
}
$para .= " -q ";
return $para;
}
1;
__END__