GEO_postprocess.pl

#!/usr/bin/perl
use strict;
#use Clone qw(clone);

unless (@ARGV == 2) {
        &USAGE;
}

sub USAGE {

die ' 

perl ~/bin/perl/GEO_postprocess.pl <GEOres.fit.txt> <GPL2995.annot.gz>



GO-file has this structure:

Gene_ID   <TAB>  GOterm,GOterm,GOterm


Prod file has this structure:

Gene_ID   <TAB>  product


';

}



# check that DESeq ran okay

my $dir = shift;
#my $go = shift;
my $prod = shift;

unless (-s "$dir") {
    die "\nSorry, the file $dir wasnt made\n";
}



# make nice scores

system "cat $dir | sed \'s/\"//g\' | tr \' \' \'\\t\' | sed \'s/ID=//g\' > $dir.scores.dat";


# make nice down
system "cat $dir.scores.dat | grep -v logFC | awk '\$6\<0.05' | awk '\$2\~\"-\"' | awk '\{print \$0\"\\tDOWN\"\}'  > $dir.DOWN";
system "cat $dir.DOWN | cut -f1 | awk \'{print \$1}\' > $dir.down.list ";
system "gzcat $prod | cut -f1,2,3  | grep -w -f  $dir.down.list  > $dir.down.list.annot ";

#print "cat $dir.scores.dat |  grep -v baseMean | awk '\$7\<0.05' | awk '\$3\~\"-\"' | awk '\{print \$0\"\\tDOWN\"\}'  > $dir.DOWN\n";
#print "cat $dir.DOWN | cut -f1 | awk \'{print \$1}\' > $dir.down.list \n";

#print  "cat $dir.scores.dat | awk '\$8\<0.05' | awk '\$3!\~\"-\"' | awk '\{print \$0\"\\tUP\"\}'  > $dir.down\n";
#system "cat $dir/lib.dat.down | cut -f2 | awk -F\'\.\' \'{print \$1}\' > $dir/lib.dat.down.list ";

# make nice up 
system "cat $dir.scores.dat | grep -v logCPM | awk '\$6\<0.05' | awk '\$2!\~\"-\"' | awk '\{print \$0\"\\tUP\"\}' > $dir.UP";
system "cat $dir.UP | cut -f1  | awk  \'{print \$1}\' > $dir.up.list ";
#print "cat $dir.scores.dat | grep -v baseMean  | awk '\$7\<0.05' | awk '\$3!\~\"-\"' | awk '\{print \$0\"\\tUP\"\}' > $dir.UP\n";
#print "cat $dir.UP | cut -f1 | awk  \'{print \$1}\' > $dir.up.list \n";
system "gzcat $prod | cut -f1,2,3 | grep -w -f  $dir.up.list  > $dir.up.list.annot ";


# make nice non-sign
system "cat $dir.scores.dat | awk '\$3\>0.05'  | awk '\{print \$0\"\\tNS\"\}' > $dir.NS";
#print "cat $dir.scores.dat | awk '\$7\>0.05'  | awk '\{print \$0\"\\tNS\"\}' > $dir.NS\n";


#__END__

system "cat $dir.UP $dir.DOWN $dir.NS > $dir.txt ";
#print "cat $dir.UP $dir.DOWN $dir.NS > $dir.txt\n";

#print "\nRunning topGO down \nperl ~/bin/perl/topGO_starter.pl $dir.down.list $go BP $prod $dir.down &\n";
#system "perl ~/bin/perl/topGO_starter.pl $dir.down.list $go BP $prod $dir.down";

#print "\nRunning topGO up \nperl ~/bin/perl/topGO_starter.pl $dir.up.list $go BP $prod $dir.up &\n";
#system "perl ~/bin/perl/topGO_starter.pl $dir.up.list $go BP $prod $dir.up";

print "All done\n";



__END__

perl ~/bin/perl/foreach.pl "cat X | grep DOWN | awk '{print 2}' > X.down" *vs*/lib.dat | sed 's/ 2/ $2/' | tail -100 > down.sh
perl ~/bin/perl/foreach.pl "cat X | grep UP | awk '{print 2}' > X.up" *vs*/lib.dat | sed 's/ 2/ $2/' | tail -100 > up.sh


# do topGO for down and up
perl ~/bin/perl/topGO_starter.pl aPS_vs_aPS/lib.dat.down ../EMU_2013_06_09.gff.GOtop BP ../EMU_2013_06_09.prod aPS_vs_aPS/lib.dat.down;
perl ~/bin/perl/topGO_starter.pl aPS_vs_MCana/lib.dat.down ../EMU_2013_06_09.gff.GOtop BP ../EMU_2013_06_09.prod aPS_vs_MCana/lib.dat.down;