CD task10 protocol
Script with all analysis steps
In this script, all the required commands for the analysis methods are listed.
Pymol visualisation
simple Pymol visalization script
mencoder "mf://*.png" -mf w=640:h=480:type=png -ofps 25 -ovc lavc -lavcopts vcodec=mpeg4:vpass=1:vbitrate=5000000:mbd=2:keyint=132:v4mv:vqmin=3:lumi_mask=0.07:dark_mask=0.2:scplx_mask=0.1:tcplx_mask=0.1:naq -o wt_movie4.avi
Significant Differences of RMSF
Provided by Marc
- !/usr/bin/perl -w
$swExit = 0;
if(@ARGV < 2){
print STDERR "statTD.pl <RMSF FILE1> <RMSF FILE2> [START] [END]\n";
exit;
}
else{
if(! -e "$ARGV[0]"){
print STDERR "File $ARGV[0] does not exist!\n";
$swExit = 1;
}
if(! -e "$ARGV[1]"){
print STDERR "File $ARGV[1] does not exist!\n";
$swExit = 1;
}
}
if(defined $ARGV[2]){
if(not defined $ARGV[3]){
print STDERR "END value missing!\n";
$swExit = 1;
}
elsif($ARGV[2] !~ m/[0-9]+/ || $ARGV[3] !~ m/[0-9]+/){
print STDERR "Problem with the ranges please check!\n";
$swExit = 1;
}
}
if($swExit){exit;}
if(defined $ARGV[2] && defined $ARGV[3] && $ARGV[2] > $ARGV[3]){
$tmp = $ARGV[2];
$ARGV[2] = $ARGV[3];
$ARGV[3] = $tmp;
}
open(FILE,$ARGV[0]);
while(<FILE>){
chomp($_);
if(/^\s*([0-9]+)\s+([0-9]+\.[0-9]+)/){
#print "$1 $2\t";
if(defined $ARGV[2] && defined $ARGV[3] && $1 >= $ARGV[2] && $1 <= $ARGV[3]){
$in1{$1} = $2;
#print "1\n";
}
elsif(not defined $ARGV[2]){
$in1{$1} = $2;
#print "$ARGV[2] $ARGV[3] 3\n";
}
}
}
close FILE;
open(FILE,$ARGV[1]);
while(<FILE>){
chomp($_);
if(/^\s*([0-9]+)\s+([0-9]+\.[0-9]+)/){
#print "$1 $2\n";
if(defined $ARGV[2] && defined $ARGV[3] && $1 >= $ARGV[2] && $1 <= $ARGV[3]) {
$in2{$1} = $2;
}
elsif(not defined $ARGV[2]){
$in2{$1} = $2;
}
}
}
close FILE;
if((keys %in1) != (keys %in2)){
print STDERR "Number of datapoints not identical!\n";
exit;
}
$value = &getPV(\%in1,\%in2);
print "$value";
if($value <= 0.001){
print "**\n";
}
elsif($value <= 0.05){
print "*\n";
}
else{
print "-\n";
}
sub getPV{
my (%data1) = %{$_[0]};
my (%data2) = %{$_[1]};
my $avg = 0;
my $cnt = 0;
my $std = 0;
my $ste = 0;
my $ratio = 0;
foreach $key (sort keys %data1){
#print "$key\n";
$avg += ($data1{$key} - $data2{$key});
$cnt++;
}
$avg /= $cnt;
foreach $key (sort keys %data1){
$std += (($data1{$key} - $data2{$key}) - $avg)**2;
}
$std /= $cnt;
$std = sqrt($std);
$ste = $std/sqrt($cnt);
$ratio = abs($avg/$ste);
open(OUT,">/tmp/rscript.tmp");
print OUT "ratio <- c($ratio);\n";
print OUT "dfree <- c($cnt);\n";
print OUT "dt(ratio,dfree);\n";
close OUT;
$value = `Rscript /tmp/rscript.tmp`;
chomp($value);
`rm -f /tmp/rscript.tmp`;
return (split/\s+/,$value)[1];
}
