comparison dataOverview.pl @ 3:80205e898861 draft default tip

New updates

2:3ed885628c9f

print OUT "$sat%\tSaturation of TA sites after cutoff filter (validInsertions/TAsites)\n";
print OUT "$inscov%\tGenome coverage by insertions (validInsertions/genomeSize)\n";
print OUT "$tacov%\tGenome coverage by TA sites (TAsites/genomeSize)\n";
print OUT "$lg_dist_ta\tLargest distance between TA sites\n";
print OUT "$lg_dist_ins\tLargest distance between insertions\n";
print OUT "\n\nOpen Reading Frames\n\n";

#Store everything to be print OUTed in array
my @table;

#Find open reading frames from fasta file
local $_  = $fasta;
my @orfSize;
my @allc; #numbers of TAs in the ORFS here.
my $blank=0; #ORFS that don't have any TA sites.
my $orfCount=0; #keep track of the number of ORFs found.
my $minSize=0; 
#Read somewhere that 99 is a good min but there is an annotated 86 bp gene for 19F
while ( /ATG/g ) {
   my $start = pos() - 3;
   if ( /T(?:AA|AG|GA)/g ) {
     my $stop = pos;
     my $size=$stop - $start;
     if ($size>=$minSize){
		 push (@orfSize,$size);
		 my $seq=substr ($_, $start, $stop - $start); 
		 my @ctemp = $seq =~ /$x/g;
		 my $countTA = @ctemp;
		 if ($countTA==0){$blank++}
		 push (@allc,$countTA);  
		 $orfCount++;  
	   }
	}
}

print OUT "\nORFs based on Fasta sequence and start (ATG) and end (TAA,TAG,TGA) codons\n";
push (@table,["Set minimum size for an ORF",$minSize]);
print OUT "$orfCount\tTotal number of ORFs found\n";
my ($minORF, $maxORF) = minmax(@orfSize);
print OUT "$minORF\tSmallest ORF\n";
print OUT "$maxORF\tLargest ORF\n";
my ($mintaORF,$maxtaORF) = minmax(@allc);
print OUT "$mintaORF\tFewest # TA sites in an ORF\n";
print OUT "$maxtaORF\tGreatest # TA sites in an ORF\n";
print OUT "$blank\tNumber of ORFs that don't have any TA sites\n";


print OUT "\nGenes using the genbank annotation file\n\n";
###Get genbank file. Find all start and stop for genes
#See how many insertions fall into genes vs intergenic regions
#Get array of coordinates for all insertions then remove insertion if it is

3:80205e898861

print OUT "$sat%\tSaturation of TA sites after cutoff filter (validInsertions/TAsites)\n";
print OUT "$inscov%\tGenome coverage by insertions (validInsertions/genomeSize)\n";
print OUT "$tacov%\tGenome coverage by TA sites (TAsites/genomeSize)\n";
print OUT "$lg_dist_ta\tLargest distance between TA sites\n";
print OUT "$lg_dist_ins\tLargest distance between insertions\n";

#Store everything to be print OUTed in array
my @table;

print OUT "\nGenes using the genbank annotation file\n\n";
###Get genbank file. Find all start and stop for genes
#See how many insertions fall into genes vs intergenic regions
#Get array of coordinates for all insertions then remove insertion if it is