diff bin/get_event_dist_fit.pl @ 1:adc0f7765d85 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/get_event_dist_fit.pl	Thu Sep 07 15:06:58 2017 -0400
@@ -0,0 +1,108 @@
+use Getopt::Long;
+use strict;
+
+use Cwd;
+my $PROG = $0;
+my $CUR_DIR = Cwd::abs_path(Cwd::cwd());
+my $PROG_ABS_PATH = Cwd::abs_path($PROG);
+my $SrcFolder=`dirname $PROG_ABS_PATH`;
+chomp($SrcFolder);
+
+#my $SrcFolder="/data/zhang/wuj/scripts/SpliceTrap.0.8/";
+my $InputFileName=$ARGV[0];
+my $OutputFileName = $ARGV[0].".hist";
+#$OutputFileName=$ARGV[1] if $ARGV[1] ne "";
+my $width=0.001;
+my $verbose=1;
+my $col=2;
+
+GetOptions (
+        'w:f'=>\$width,
+        'c:i'=>\$col,
+        'v'=>\$verbose
+);
+
+$width=$width*1;
+my $binnum=1/$width;
+$col=$col-1;
+
+my @CAratios;
+my @CSratios;
+my @ADratios;
+my @AAratios;
+my @AIratios;
+my @IRratios;
+
+open(Input, $InputFileName);
+while(my $line=<Input>)
+{
+        next if($line=~/^#/);
+        chomp($line);
+        my @array=split(/\s/,$line);
+	next if($array[$col]<=0.001 or $array[$col]>=0.999);
+#        push( @CAratios,$array[$col]) if($array[0]=~/^C[AS]/ or $array[0]=~/^ME/);
+	push( @CAratios,$array[$col]) if($array[0]=~/^CA/ or $array[0]=~/^ME/);
+	push( @CSratios,$array[$col]) if($array[0]=~/^CS/);
+	push( @ADratios,$array[$col]) if($array[0]=~/^AD/);
+	push( @AAratios,$array[$col]) if($array[0]=~/^AA/);
+	push( @AIratios,$array[$col]) if($array[0]=~/^AI/);
+	push( @IRratios,$array[$col]) if($array[0]=~/^IR/);
+
+}
+
+close(Input);
+
+open(tmpFile, ">$InputFileName.tmpca");
+for(my $i=0;$i<@CAratios;$i++)
+{
+	print tmpFile $CAratios[$i],"\n";
+}
+close(tmpFile);
+open(tmpFile, ">$InputFileName.tmpcs");
+for(my $i=0;$i<@CSratios;$i++)
+{
+        print tmpFile $CSratios[$i],"\n";
+}
+close(tmpFile);
+
+
+open(tmpFile, ">$InputFileName.tmpad");
+for(my $i=0;$i<@ADratios;$i++)
+{
+        print tmpFile $ADratios[$i],"\n";
+}
+close(tmpFile);
+
+open(tmpFile, ">$InputFileName.tmpaa");
+for(my $i=0;$i<@AAratios;$i++)
+{
+        print tmpFile $AAratios[$i],"\n";
+}
+close(tmpFile);
+
+open(tmpFile, ">$InputFileName.tmpai");
+for(my $i=0;$i<@AIratios;$i++)
+{
+        print tmpFile $AIratios[$i],"\n";
+}
+close(tmpFile);
+
+open(tmpFile, ">$InputFileName.tmpir");
+for(my $i=0;$i<@IRratios;$i++)
+{
+        print tmpFile $IRratios[$i],"\n";
+}
+close(tmpFile);
+
+system("R --slave --args $InputFileName.tmpca <$SrcFolder/beta_fit.R");
+system("R --slave --args $InputFileName.tmpad <$SrcFolder/beta_fit.R");
+system("R --slave --args $InputFileName.tmpaa <$SrcFolder/beta_fit.R");
+#system("R --slave --args $InputFileName.tmpai <$SrcFolder/R/beta_fit.R");
+system("R --slave --args $InputFileName.tmpir <$SrcFolder/beta_fit.R");
+system("R --slave --args $InputFileName.tmpcs <$SrcFolder/beta_fit.R");
+
+system("echo '#Width:$width' >$InputFileName.fit.hist");
+#system("paste $InputFileName.tmpca.fit $InputFileName.tmpad.fit $InputFileName.tmpaa.fit $InputFileName.tmpai.fit $InputFileName.tmpir.fit $InputFileName.tmpcs.fit >>$InputFileName.fit.hist");
+
+system("paste $InputFileName.tmpca.fit $InputFileName.tmpad.fit $InputFileName.tmpaa.fit $InputFileName.tmpir.fit $InputFileName.tmpcs.fit >>$InputFileName.fit.hist");
+#system("rm $InputFileName.tmpca* $InputFileName.tmpad* $InputFileName.tmpaa* $InputFileName.tmpai* $InputFileName.tmpir* ");