G::Tools

Fasta

Methods description

Methods code

    &opt_default(qr=>'off',input=>"file");
    my @param;
    my @tmp;
    foreach(@_){
        if($_ eq '-a' || $_ eq '-A' || $_ eq '-B' || $_ eq '-f' || $_ eq '-g' ||
           $_ eq '-h' || $_ eq '-H' || $_ eq '-i' || $_ eq '-L' || $_ eq '-n' || 
           $_ eq '-o' || $_ eq '-p' || $_ eq '-Q' || $_ eq '-q' || $_ eq '-r' ||
           $_ eq '-S' || $_ eq '-1' || $_ eq '-3' ){
	    push(@param,$_);
        }
        else{
            push(@tmp,$_);
        }
    }
    @_=@tmp;
    my @args=opt_get(@_);

    my $qr=&opt_val("qr");
    my $input=&opt_val("input");
    my $data;
    my $file;
    my $seq;
    my %opt;
    my $param;
    my $num;

    $data=shift @args;
    if($input eq 'seq'){
	$seq=shift @args;
	opendir(DIR,'/tmp');
	@tmp=readdir(DIR);
	$num=$##tmp+1+time;
	@tmp=keys(%$seq);
	open(FILE,'>/tmp/fasta_'.$num.'.seq');
	print FILE ">$tmp[0]\n";
	print FILE $$seq{"$tmp[0]"},"\n";
	close(FILE);
	$file='/tmp/fasta_'.$num.'.seq'; 
    }
    else{
	$file=shift @args;
    }

    $opt{E}=&opt_val("E");
    $opt{O}=&opt_val("O");
    $opt{b}=&opt_val("b");
    $opt{c}=&opt_val("c");
    $opt{d}=&opt_val("d");
    $opt{F}=&opt_val("F");
    $opt{j}=&opt_val("j");
    $opt{l}=&opt_val("l");
    $opt{M}=&opt_val("M");
    $opt{m}=&opt_val("m");
    $opt{R}=&opt_val("R");
    $opt{s}=&opt_val("s");
    $opt{w}=&opt_val("w");
    $opt{x}=&opt_val("x");
    $opt{X}=&opt_val("X");
    $opt{y}=&opt_val("y");
    $opt{z}=&opt_val("z");

    foreach(sort keys(%opt)){
	next if($opt{$_} eq '');
	push(@param,'-'.$_);
	push(@param,$opt{$_});
    }
    $param=join(' ',@param);

    system('fasta33',"$data","$file",@param) if($qr eq "off");
    system('qr',"fasta33 $data $file $param") if($qr eq "on");

    unlink('/tmp/fasta_'.$num.'.seq') if($input eq 'seq' && $qr ne 'on');

    return "$data $file $param";
}

sub DESTROY {
    my $self = shift;
}

1;
__END__
## Below is the stub of documentation for your module. You better edit it!

=head1 NAME

G::Tools::Fasta - Perl extension for blah blah blah

=head1 SYNOPSIS

  use G::Tools::Fasta;
  blah blah blah

=head1 DESCRIPTION

Stub documentation for G::Tools::Fasta was created by h2xs. It looks like the
author of the extension was negligent enough to leave the stub
unedited.

Blah blah blah.

=head1 AUTHOR

A. U. Thor, a.u.thor@a.galaxy.far.far.away

=head1 SEE ALSO

perl(1).

=cut

    my $pkg = shift;
    my $filename = shift;
    my $option = shift;
    my $this;

    return $this;

General documentation