Difference between revisions of "CD task10 protocol"

From Bioinformatikpedia
(Pymol visualisation)
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-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
 
-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
 
-o wt_movie4.avi
  +
  +
== Significant Differences of RMSF==
  +
  +
Provided by Marc
  +
  +
  +
#!/usr/bin/perl -w
  +
$swExit = 0;
  +
  +
if(@ARGV < 2){
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print STDERR "statTD.pl <RMSF FILE1> <RMSF FILE2> [START] [END]\n";
  +
exit;
  +
}
  +
else{
  +
if(! -e "$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 = $ARGV[2];
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$ARGV[2] = $ARGV[3];
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$ARGV[3] = $tmp;
  +
}
  +
  +
  +
open(FILE,$ARGV[0]);
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while(<FILE>){
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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];
  +
}

Revision as of 16:00, 14 August 2012



Script with all analysis steps

In this script, all the required commands for the analysis methods are listed.

analysis.sh

Pymol visualisation

simple Pymol visalization script

create_pymol_vis.py


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


  1. !/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]; }