G::Tools

HMMER

Summary Included libraries Package variables Synopsis Description General documentation Methods

Summary
G::Tools::HMMER - Perl extension for blah blah blah
Package variables top
Globals (from use vars definitions)
@EXPORT
$VERSION
@EXPORT_OK
Included modulestop
G::Messenger
SubOpt
strict
Inherit top
AutoLoader Exporter
Synopsistop
  use G::Tools::HMMER;
blah blah blah
Descriptiontop
Stub documentation for G::Tools::HMMER was created by h2xs. It looks like the
author of the extension was negligent enough to leave the stub
unedited.

Blah blah blah.
Methodstop
DESTROYNo descriptionCode
_hmmpfamNo descriptionCode
newNo descriptionCode

Methods description


Methods code

DESTROYdescriptiontopprevnext
sub DESTROY {
    my $self = shift;
}
_hmmpfamdescriptiontopprevnext
sub _hmmpfam {
    &opt_default(qr=>'off',input=>"file",filename=>"hmmpfam.hmm",output=>"f");
    my @param;
    my @tmp;
    foreach(@_){
	if($_ eq '-n' || $_ eq '--forward' || $_ eq '--null2' || $_ eq '--pvm' ||$_ eq '--xnu'){
	    push(@param,$_);
	}
	else{
	    push(@tmp,$_);
	}
    }
    @_=@tmp;
    my @args=opt_get(@_);

    my $qr=&opt_val("qr");
    my $input=&opt_val("input");
    my $output=&opt_val("output");
    my $data=shift @args;
    my $file;
    my $filename;
    my $seq;
    my $param;
    my %opt;
    my $num;

    if($input eq "seq"){
	$seq=shift @args;
	opendir(DIR,'/tmp');
	@tmp=readdir(DIR);
	$num=$##tmp+1+time;
@tmp=keys(%$seq); open(FILE,'>/tmp/hmmpfam_'.$num.'.seq'); print FILE ">$tmp[0]\n"; print FILE $$seq{$tmp[0]},"\n"; close(FILE); $file='/tmp/hmmpfam_'.$num.'.seq'; $filename=&opt_val("filename"); } else{ $file=shift @args; $filename=$file.'.hmm'; } $opt{A}=&opt_val("A"); $opt{E}=&opt_val("E"); $opt{T}=&opt_val("T"); $opt{Z}=&opt_val("Z"); $opt{-cpu}=&opt_val('-cpu'); $opt{-domE}=&opt_val('-domE'); $opt{-domT}=&opt_val('-domT'); foreach(sort keys(%opt)){ next if($opt{$_} eq ''); push(@param,'-'.$_); push(@param,$opt{$_}); } $param=join(" ",@param); if($qr eq "on"){ system('qr',"hmmpfam $param $data $file") if($output eq "stdout"); system('qr',"hmmpfam $param $data $file > $filename") if($output ne "stdout"); } else{ system("hmmpfam $param $data $file") if($output eq "stdout"); system("hmmpfam $param $data $file > $filename") if($output ne "stdout"); } unlink('/tmp/hmmpfam_'.$num.'.seq') if($input eq "seq" && $qr ne 'on'); return "$param $data $file";
}
newdescriptiontopprevnext
sub new {
    my $pkg = shift;
    my $filename = shift;
    my $option = shift;
    my $this;

    return $this;
}

General documentation

AUTHOR top
A. U. Thor, a.u.thor@a.galaxy.far.far.away
SEE ALSO top
perl(1).