None available.
sub _read_master
{ my (%ma2ec, %ma2jw);
open(FILE, '/home/gaou/mori_data_0805/glang/MasterREFE4K10NEW.txt') || die($!);
while(<FILE>){
chomp;
my ($maid, $ecid, $jwid, undef) = split(/\t/, $_, 4);
$ma2ec{$maid} = $ecid;
$ma2jw{$maid} = $jwid;
}
close(FILE);
return (\%ma2ec,\% ma2jw);} | sub ma_filter
{ my ($tmp1, $tmp2) = _read_master();
my %ma2ec = %$tmp1;
my %ma2jw = %$tmp2;
opt_default(xmax=>1024, xmin=>-1024, ymax=>1024, -ymin=>-1024);
my @args = opt_get(@_);
my $file = shift @args;
my $xmax = opt_val("xmax");
my $xmin = opt_val("xmin");
my $ymax = opt_val("ymax");
my $ymin = opt_val("ymin");
my $newfile = $file;
if ($newfile =~ /-norm/){
$newfile =~ s/-norm/-filter/g;
}else{
$newfile .= '-filter';
}
open(FILE, $file) || die ($!);
open(OUT, '>' . $newfile) || die ($!);
my @result;
while(<FILE>){
my $line = $_;
chomp;
my ($maid, $ecid, $jwid, $cy3s, $cy3b, $cy5s, $cy5b, $logn, $logm) =
split (/\t/, $_, 9);
next if ($logn eq '-' || $logm eq '-');
if($logn >= $ymin && $logn <= $ymax && $logm >= $xmin && $logn <= $xmax){
push(@result, "$maid $logn");
print OUT $line;
}
}
close(FILE);
close(OUT);
return ($newfile,\@ result);} | sub ma_normalize
{ my ($tmp1, $tmp2) = _read_master();
my %ma2ec = %$tmp1;
my %ma2jw = %$tmp2;
my $name;
my $flag = 0;
my %data;
my $filename = shift;
open(FILE, $filename) || die($!);
while(<FILE>){
if(/^Control image file:\s+(.*?)\.tif/){
$name = $1;
}elsif(/^Begin Extracted Data/){
$flag = 1;
}elsif(/^\d/ && $flag){
my (undef, undef, undef, undef, $id,
undef, undef, undef, $cy3s, $cy3b,
undef, undef, undef, undef, undef,
undef, undef, undef, undef, undef,
$cy5s, $cy5b, undef
) = split(/\s+/, $_, 24);
$data{$id} .= "$cy3s $cy3b $cy5s $cy5b:";
}
}
close(FILE);
my %id2norm;
my %id2ri;
my (@R, @I);
my %multi;
open(OUT, ">$name-norm.txt") || die($!);
foreach my $id (sort keys %data){
foreach my $line (split(/:/, $data{$id})){
next if ($ma2jw{$id} eq '');
if (length $line){
my ($cy3s, $cy3b, $cy5s, $cy5b) = split(/\s/, $line, 4);
my $logn = '-';
my $cy3 = $cy3s-$cy3b;
my $cy5 = $cy5s-$cy5b;
unless(($cy3s-$cy3b)/($cy5s-$cy5b) <= 0){
$logn = log(($cy3s-$cy3b)/($cy5s-$cy5b))/log(2);
my $logm = log($cy3*$cy5)/log(10);
printf OUT "%s\t%s\t%s\t%.4f\t%.4f\t%.4f\t%.4f\t%f\t%f\n",
$id, $ma2ec{$id}, $ma2jw{$id},
$cy3s, $cy3b, $cy5s, $cy5b,
$logn, $logm;
if ($logn > $id2norm{$id}){
$id2norm{$id} = $logn;
$id2ri{$id} = log(($cy3s-$cy3b)*($cy5s-$cy5b))/log(10);
}
push(@R, log(($cy3s-$cy3b)*($cy5s-$cy5b))/log(10));
push(@I, $logn);
$multi{$id} .= "$logn ";
next;
}
printf OUT "%s\t%s\t%s\t%.4f\t%.4f\t%.4f\t%.4f\t-\t-\n",
$id, $ma2ec{$id}, $ma2jw{$id},
$cy3s, $cy3b, $cy5s, $cy5b;
unless($id2norm{$id}){
$id2norm{$id} = -1024;
$id2ri{$id} = -1024;
$multi{$id} .= "-1024 ";
}
}
}} | sub ma_rfilter
{ require Statistics::Descriptive;
my ($tmp1, $tmp2) = _read_master();
my %ma2ec = %$tmp1;
my %ma2jw = %$tmp2;
opt_default(z=>1);
my @args = opt_get(@_);
my $file = shift @args;
my $z = opt_val("z");
my $newfile = $file;
if ($newfile =~ /-norm/){
$newfile =~ s/-norm/-rfilter/g;
}elsif($newfile =~ /-filter/){
$newfile =~ s/-filter/-rfilter/g;
}else{
$newfile .= '-rfilter';
}
my %ratio;
my $prev = '';
open(FILE, $file) || die ($!);
open(OUT, '>' . $newfile) || die ($!);
while(<FILE>){
my $line = $_;
chomp;
my ($maid, $ecid, $jwid, $cy3s, $cy3b, $cy5s, $cy5b, $logn, $logm) =
split (/\t/, $_, 9);
next if ($logn eq '-' || $logm eq '-');
my ($pmaid, $pecid, $pjwid, $pcy3s, $pcy3b, $pcy5s, $pcy5b, $plogn, $plogm) =
split (/\t/, $_, 9);
if ($pmaid eq $maid){
$ratio{$pmaid} = $plogn / $logn;
}else{
$prev = $line;
}
}
seek(FILE, 0, 0);
my $stat = Statistics::Descriptive::Full->new();
$stat->add_data(values %ratio);
my $mean = $stat->mean();
my $sd = $stat->standard_deviation();
$prev = '';
while(<FILE>){
my $line = $_;
chomp;
my ($maid, $ecid, $jwid, $cy3s, $cy3b, $cy5s, $cy5b, $logn, $logm) =
split (/\t/, $_, 9);
next if ($logn eq '-' || $logm eq '-');
my ($pmaid, $pecid, $pjwid, $pcy3s, $pcy3b, $pcy5s, $pcy5b, $plogn, $plogm) =
split (/\t/, $_, 9);
if ($pmaid eq $maid && ($ratio{$pmaid} - $mean) >= $z * $sd){
print OUT $line, $prev;
}else{
$prev = $line;
}
}
close(FILE);
close(OUT);
return $newfile;} |