None available.
sub _fasta
{ &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";
}
1;} |