--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compRegions.pl	Tue Mar 28 21:51:45 2017 -0400
@@ -0,0 +1,179 @@
+#!/usr/bin/perl -w
+
+#Margaret Antonio 17.01.10 For GALAXY
+
+use Data::Dumper;
+use strict;
+use Getopt::Long;
+use Statistics::Distributions;
+no warnings;
+
+#ASSIGN INPUTS TO VARIABLES USING FLAGS
+our ($input1, $input2, $help,$out,$round,$l1, $l2);
+
+GetOptions(
+'input1:s' => \$input1,
+'input2:s' => \$input2,
+'h' => \$help,
+'o:s' =>\$out,
+'r:i'=> \$round,
+'l1:s'=> \$l1,
+'l2:s'=> \$l2,
+);
+
+sub print_usage() {
+    print "\n####################################################################\n";
+    print "\n";
+    print "compWindows.pl: compare regions outputted by the slidingWindow tool\n\n";
+    print "DESCRIPTION: Takes two slidingWindows.csv files and compares them by\n";
+    print "calculating the difference in mean fitness, the pval for each gene.\n";
+    print "Example: compare control vs antibiotic, where both from same strain (genome).\n";
+    print "Note: For different strains/genomes, use compStrains for a gene comparison.pl\n";
+    
+    print "\nUSAGE:\n";
+    print "perl compGenes.pl -d inputs/ -l cond1,cond2 -r 2 -o comp-cond1cond2_date.csv\n";
+    
+    print "\nREQUIRED:\n";
+    print " -d\tDirectory containing two slidingWindow.csv files (output of\n";
+    print "   \tslidingWindow tool)\n";
+    print "   \tOR\n";
+    print "   \tIn the command line (without a flag), input the name(s) of\n";
+    print "   \ttwo files.\n";
+    
+    print "\nOPTIONAL:\n";
+    print " -h\tPrints usage and exits program\n";
+    print " -o\tOutput file for comparison data. Default: label1label2.csv\n";
+    print " -r\tRound final output numbers to this number of decimals\n";
+    print " -s\tColumn number to sort by. Default: difference of means\n";
+    print " -l\tLabels for input files. Default: filenames\n";
+    print "   \tTwo strings, comma separated (i.e. -l expt1,expt2).\n";
+    print "   \tOrder should match file order.\n";
+    
+    print " \n~~~~Always check that file paths are correctly specified~~~~\n";
+    print "\n##################################################################\n";
+}
+if ($help){
+    print_usage();
+    exit;
+}
+
+
+
+#THE @files ARRAY WILL CONTAIN INPUT FILE NAMES
+my @files=($input1,$input2);
+
+#GET LABELS: USE (-l) OR USE FILNEAMES AS LABELS FOR COLUMNS IN OUTPUT FILE
+
+my @labels=($l1,$l2);
+
+#INDICES 0:start	1:end	2:mutants	3:insertions	4:TA_sites	5:ratio	6:p-value
+#7:average	8:variance	9:stdev	10:stderr	11:genes	12:fit-mean
+
+#CHECK IF REQ. VARIABLES WERE DEFINED USING FLAGS. IF NOT THEN USE DEFAULT VALUES
+
+if (!$out) {$out="comp.".$labels[0].$labels[1].".csv"}
+if (!$round){$round='%.4f'}
+
+#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;
+for (my $i=0; $i<2; $i++){
+    print "File #",$i+1,"\t";
+    my $file=$files[$i];
+    print $file,"\n";
+    
+    open(DATA, '<', $file) or (print "Could not open '$file'\n" and print_usage() and exit);
+    
+    #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 $head=<DATA>;
+    my @cols=split(',',$head);
+    for (my $j=0;$j<scalar @cols;$j++){
+        my $colname=$cols[$j];
+        chomp($colname);
+        $cols[$j]=$colname.'-'.$labels[$i];
+        print $cols[$j],"\n";
+    }
+    push (@header,@cols);
+
+    while (my $entry = <DATA>) {
+        chomp $entry;
+        my @line=split(",",$entry);
+        if (!$line[11]){
+            $line[11]="NA";
+        }
+        my ($start,$end,$mutants,$insertions,$TAsites,$ratio,$pval,$avg,$var,$sd,$se,$genes)=@line;
+        $avg=sprintf("%.3f",$avg);
+
+        #if (!$line[6]){
+        #    $line[6]=0;
+        #}
+        #@line=@line[0,1,2,3,4,5,6];
+
+        
+        #PUT GENE AND INFO INTO THE HASH FOR EXISTING KEY (1ST FILE) OR CREATE NEW KEY (2ND FILE)
+        my $key=$start;
+        if(!exists $all{$key}){
+            my @info;
+            push (@info,@line);
+            $all{$key}=\@info;
+        }
+        #Otherwise the window existed for the prior file, and now need to calcualte extra stats
+        else{
+            my @info=@{$all{$key}};
+            my ($start2,$end2,$mutants2,$insertions2,$TAsites2,$ratio2,$pval2,$avg2,$var2,$sd2,$se2,$genes2)=@info;
+            my $diff=sprintf("$round",($avg-$avg2));
+            my $df=$insertions+$insertions2-2;
+            my $tdist;
+            my $pval;
+
+            # CHECK TO MAKE SURE ALL VARIABLES IN TDIST,PVAL CALCULATIONS ARE NUMBERS AND NO
+            # ZEROS (0) IN THE DENOMINATOR
+            
+            if ($se eq "NA" or $se2 eq "NA" or $sd eq "NA" or $sd2 eq "NA" or $insertions==0 or $insertions2==0 or $sd==0 or $sd2==0 or $df<=0){
+                ($tdist,$pval)=(" "," ");
+            }
+            else{
+                $tdist=sqrt((($diff)/(sqrt((($sd**2)/$insertions)+(($sd2**2)/$insertions2))))**2);
+                $pval=Statistics::Distributions::tprob($df,$tdist);
+            }
+            push (@info,@line,$diff,$df,$tdist,$pval);
+            $all{$key}=\@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
+
+my $sortkey=26; #default: sort by difference of means
+
+my @sorted = sort { $b->[$sortkey] <=> $a->[$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, '>',"$out";
+print OUT (join(',',@header),"\n");
+foreach (@sorted){
+    my @woo=@{$_};
+    print OUT join(',',@woo),"\n";
+}
+close OUT;
+
+