--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compGenes.pl	Wed Mar 29 14:39:36 2017 -0400
@@ -0,0 +1,187 @@
+#!/usr/bin/perl -w
+
+#Margaret Antonio 17.01.06 without essentiality. For original, unmodified aggregate.pl output (where unique insertions are not included). 
+
+use Getopt::Long;
+use Statistics::Distributions;
+use strict;
+use autodie;
+no warnings;
+
+#no warnings;
+
+#ASSIGN INPUTS TO VARIABLES USING FLAGS
+our ($input1, $input2, $h, $out, $sortkey, $round, $l1, $l2, $outfile);
+
+GetOptions(
+'input1:s' => \$input1,
+'input2:s' => \$input2,
+'h' => \$h,
+'o:s' =>\$outfile,
+'r:i'=> \$round,
+
+);
+
+sub print_usage() {
+    print "\n####################################################################\n";
+    
+    print "compGenes: compare genes for an organism under different conditions\n\n";
+    print "DESCRIPTION: Takes two aggregate.pl outputs and compares them by\n";
+    print "calculating the difference in mean fitness for each gene.\n";
+    print "Example: compare organism in presence of control vs antibiotic.\n";
+    print "Note: For different strains/genomes, use compStrains.pl\n";
+    
+    print "\nUSAGE:";
+    print "perl compGenes.pl -d inputs/ \n\n";
+    
+    print "REQUIRED:\n";
+    print " -d\tDirectory containing all input files (files from\n";
+    print "   \taggregate script)\n";
+    print "   \tOR\n";
+    print "   \tIn the command line (without a flag), input the name(s) of\n";
+    print "   \ttwo files containing aggregate gene fitness values. \n\n";
+    
+    print "OPTIONAL:\n";
+    print " -h\tPrints usage and exits program\n";
+    print " -o\tOutput file for comparison data. Default: label1label2.csv\n";
+    print " -r\tRound final output numbers to this number of decimals\n";
+    print " -l1\tLabels for input files. Default: filenames\n";
+    print "   \tTwo strings, comma separated (i.e. -l expt1,expt2).\n";
+    print "   \tOrder should match file order.\n";
+    
+    print " \n~~~~Always check that file paths are correctly specified~~~~\n";
+    print "\n##################################################################\n";
+
+}
+
+# Check if help needed or if improper inputs
+
+if ($h){
+    print_usage();
+    exit;
+}
+
+if (! $outfile){
+    $outfile="geneComp.csv"
+}
+$round = '%.4f';
+
+my @files=($input1,$input2);
+
+#GET LABELS: USE (-l) OR USE FILNEAMES AS LABELS FOR COLUMNS IN OUTPUT FILE
+
+my @labels=($l1,$l2);
+
+#CHECK IF REQ. VARIABLES WERE DEFINED USING FLAGS. IF NOT THEN USE DEFAULT VALUES
+
+#$out="comp.".$labels[0].$labels[1].".csv";
+
+#READ INPUT FILES AND PUT GENE INFO FROM EACH LINE INTO HASH %all WHERE KEY=GENE_ID AND
+#VALUE=GENE INFO (MEAN FITNESS, # INSERTIONS, ETC.)
+
+my %all;
+my @header;
+
+#OPEN TWO COMPARISON FILES, ONE PER LOOP
+for (my $i=0; $i<2; $i++){
+    print "File #",$i+1,"\t";
+    my $file=$files[$i];
+    print $file,"\n";
+    
+    open(DATA, '<', $file) or die "Could not open '$file'\n";
+    
+    #EXTRACT THE HEADER (COLUMN NAMES) OF THE FILE AND KEEP FOR OUTPUT HEADER
+    #APPEND FILE NAME OR GIVEN LABEL (-l) TO COLUMN NAME SO ITS DIFFERENT FROM OTHER INPUT FILE
+    
+    my $head=<DATA>;
+    my @temp = split("\n",$head);
+    $head = $temp[0];
+    
+    my @cols=split(',',$head);
+    @cols = @cols[0,1,2,3,4,5];
+    for (my $j=0;$j<scalar @cols;$j++){
+        $cols[$j]=$cols[$j].'-'.$labels[$i];
+    }
+    push (@header,@cols);
+    while (my $entry = <DATA>) {
+        chomp $entry;
+        my @line=split(",",$entry);
+        if (!$line[5]){
+            $line[5]="NA";
+        }
+        if (!$line[6]){
+            $line[6]=0;
+        }
+        @line=@line[0,1,2,3,4,5];
+        my $gene=$line[0];
+        chomp($gene);
+        
+        #PUT GENE AND INFO INTO THE HASH FOR EXISTING KEY (1ST FILE) OR CREATE NEW KEY (2ND FILE)
+        
+        if (!exists $all{$gene}){
+            my @info;
+            push (@info,@line);
+            $all{$gene}=\@info;
+        }
+        else{
+            my @info=@{$all{$gene}};
+            push (@info,@line);
+            my $diff=sprintf("$round",($info[1]-$info[7]));
+            my $total1=$info[2];
+            my $total2=$info[8];
+            my $sd1=$info[3];
+            my $se1=$info[4];
+            my $sd2=$info[9];
+            my $se2=$info[10];
+            my $df=$total1+$total2-2;
+            my $tdist;
+            my $pval;
+            
+            # CHECK TO MAKE SURE ALL VARIABLES IN TDIST,PVAL CALCULATIONS ARE NUMBERS AND NO
+            # ZEROS (0) IN THE DENOMINATOR
+            
+            if ($se1 eq "X" or $se2 eq "X" or $sd1 eq "X" or $sd2 eq "X" or $total1==0 or $total2==0 or $sd1==0 or $sd2==0 or $df<=0){
+                ($tdist,$pval)=("NA","NA");
+            }
+            else{
+                $tdist=sqrt((($diff)/(sqrt((($sd1**2)/$total1)+(($sd2**2)/$total2))))**2);
+                
+                $pval=Statistics::Distributions::tprob($df,$tdist);
+            }
+            push (@info,$diff,$df,$tdist,$pval);
+            $all{$gene}=\@info;
+        }
+    }
+    close DATA;
+}
+
+#READ ALL HASH CONTENTS INTO 2D ARRAY FOR EASY SORTING AND PRINTING TO OUT FILE
+my @unsorted;
+
+foreach my $entry (keys %all) {
+    my @info=@{$all{$entry}};
+    my @temp;
+    push (@temp,@info);
+    push (@unsorted,\@temp);
+}
+
+#SORT GENES BY PVALUE OR FITNESS DEPENDING ON WHICH FLAG WAS USED IN COMMANDLINE
+
+$sortkey=15; #default: sort by difference of means
+
+my @sorted = sort { $a->[$sortkey] <=> $b->[$sortkey] } @unsorted;
+
+#ADD NEW FIELDS TO HEADER (COLUMN NAMES)
+my $field="Mean".$labels[0].'.'.$labels[1];
+push (@header,$field,"DOF","TDIST","PVALUE");
+
+#PRINT TO OUT FILE
+open OUT, '>',"$outfile";
+print OUT (join(',',@header),"\n");
+foreach (@sorted){
+    my @woo=@{$_};
+    print OUT join(',',@woo),"\n";
+    }
+close OUT;
+
+