G::Tools
HMMER
G::Tools::HMMER - Perl extension for blah blah blah
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Globals (from use vars definitions) |
@EXPORT |
$VERSION |
@EXPORT_OK |
use G::Tools::HMMER; blah blah blah
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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.
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DESTROY | No description | Code |
_hmmpfam | No description | Code |
new | No description | Code |
Methods description
Methods code
sub DESTROY
{ my $self = shift;
}
sub _hmmpfam
{ &opt_default(qr=>'off',input=>"file",filename=>"hmmpfam.hmm",output=>"f");
my @param;
my @tmp;
foreach(@_){
if($_ 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";
}
sub new
{ my $pkg = shift;
my $filename = shift;
my $option = shift;
my $this;
return $this;
}
General documentation