--- a/compGenes.pl	Wed Mar 29 19:39:51 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,185 +0,0 @@
-#!/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";
-        }
-
-        @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;
-
-