--- a/compStrains.pl	Wed Mar 29 14:18:07 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,207 +0,0 @@
-#!/usr/bin/perl -w
-
-#Margaret Antonio 16.01.13
-
-#DESCRIPTION: Takes two aggregate.pl outputs and compares them using mean difference, pval for each
-#gene. Can compare, for example, 19F in glucose and TIGR4 in glucose.
-#DIFFERENT GENOMES (ie. diff. strains).
-#Requires CONVERSION FILE
-
-#USAGE: perl compStrains.pl -c <conversion.csv> <options>
-    #[<aggregateFile1.csv aggregateFile2.csv> OR -indir <indir/>]
-
-use Data::Dumper;
-use strict;
-use Getopt::Long;
-use warnings;
-use File::Path;
-use File::Basename;
-use Statistics::Distributions;
-
-#ASSIGN INPUTS TO VARIABLES USING FLAGS
-our ($input1,$input2,$out,$sortkey,$round,$l1,$l2,$cfile);
-GetOptions(
-'o:s' =>\$out,
-'s:i' => \$sortkey,
-'r:i'=> \$round,
-'l1:s'=> \$l1,
-'l2:s'=> \$l2,
-'c:s'=> \$cfile,
-'input1:s'=>\$input1,
-'input2:s'=>\$input2
-);
-
-sub print_usage() {
-    print "\n";
-    print "\n##################################################################\n";
-    print "compStrains.pl: compare genes from a tn-seq experiment\n";
-    print "\tfor two DIFFERENT strains/genomes using aggregate files\n";
-    
-    print "\nDESCRIPTION: Takes two aggregate.pl outputs and compares them by\n";
-    print "calculating the difference in mean fitness.\n";
-    
-    print "Example: two strains tested under same condition.\n";
-    print "Note: For same strains (genomes), use compGenes.pl\n";
-    
-    print "\nUSAGE:\n";
-    print "perl compStrains.pl -c conversion.csv -d inputs/\n";
-    
-    print "\nREQUIRED:\n";
-    print " -d\tDirectory containing all input files (files from\n";
-    print "   \taggregate fitness 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 " -c\tConversion file: two columns with homologs for both organisms\n";
-
-    print "\nOPTIONAL:\n";
-    print " -h\tPrints usage and exits program\n";
-    print " -o\tOutput file for comparison data. Default: label1label2.csv\n";
-    print " -s\tSort output by this index of the file (indices begin at 0).\n";
-    print "   \tDefault: by mean\n";
-    print " -r\tRound final output numbers to this number of decimals\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";
-}
-
-#THE @files ARRAY WILL CONTAIN INPUT FILE NAMES
-my @files=($input1,$input2)
-
-#GET LABELS:
-my @labels = ($l1,$l2);
-
-
-#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'}
-
-#OPEN INPUTTED AGGREGATE GENE FILES AND STORE THEIR CONTENTS INTO TWO HASHES
-#FILE1 GOES INTO HASH %ONE AND FILE2 GOES INTO HASH %TWO.
-
-#FILE1 OPENING ---> %one WHERE KEY:VALUE IS GENE_ID:(GENE_ID,INSERTIONS,MEAN,ETC.)
-my @header;
-my %one;
-
-open (F1,'<',$files[0]);
-
-#STORE COLUMN NAMES (FIRST LINE OF FILE1) FOR HEADER AND APPEND LABELS
-my $head=<F1>; #the header in the file
-my @cols=split(',',$head);
-@cols=@cols[0,1,2,3,4,5,6]; #get rid of blank columns
-for (my $j=0;$j<scalar @cols;$j++){
-    $cols[$j]=$cols[$j].'-'.$labels[0];   #mark each column name with file it comes from
-}
-push (@header,@cols);
-
-while (my $line=<F1>){
-    chomp $line;
-    my @info=split(",",$line);
-    #Only keep the first 7 columns (Ones about blanks aren't needed for comparisons)
-    @info=@info[0,1,2,3,4,5,6];
-    #Sometimes genes that don't have a gene name can't be blank, so fill with NA
-    if (!$info[5]){
-        $info[5]="NA";
-    }
-    #If there are no insertions in the column "total", then make it =0 rather than blank
-    if (!$info[6]){
-        $info[6]=0;
-    }
-    $one{$info[0]}=\@info;
-}
-close F1;
-
-#FILE2 OPENING ---> %two WHERE KEY:VALUE IS GENE_ID:(GENE_ID,INSERTIONS,MEAN,ETC.)
-
-my %two;
-open (F2,'<',$files[1]);
-
-#STORE COLUMN NAMES (FIRST LINE OF FILE2) FOR HEADER AND APPEND LABELS
-$head=<F2>; #the header in the file
-@cols=split(',',$head);
-@cols=@cols[0,1,2,3,4,5,6]; #get rid of blank columns
-for (my $j=0;$j<scalar @cols;$j++){
-    $cols[$j]=$cols[$j].'-'.$labels[1];   #mark each column name with file it comes from
-}
-push (@header,@cols);
-
-while (my $line=<F2>){
-    chomp $line;
-    my @info=split(",",$line);
-    @info=@info[0,1,2,3,4,5,6];
-    if (!$info[5]){
-        $info[5]="NA";
-    }
-    if (!$info[6]){
-        $info[6]=0;
-    }
-    $two{$info[0]}=\@info;
-}
-close F2;
-
-
-#READ CONVERSION FILE INTO ARRAY.
-#Conversion file must have strain 1 for file 1 in column 1 (index 0) and
-    #strain 2 for file 2 in column 2 (index 1)
-    #conversion file must be tab delimited with no NA fields
-#If homologs (exist then take info from hashes (%one and %two) by referring to gene_id in KEY
-
-my @all; #store all homologs in this hash
-open (CONV,'<',$cfile);
-while (my $line=<CONV>){
-    chomp $line;
-    my @genes=split("\t",$line);   #Array @genes will contain two genes (SP_0000,SPT_0000)
-    if (scalar @genes==2 and $genes[0] ne "" and $genes[1] ne ""){
-        my @info;
-        my @oneArray=@{$one{$genes[0]}};
-        my @twoArray=@{$two{$genes[1]}};
-        push (@info,@oneArray,@twoArray);
-        my $diff=sprintf("$round",($info[1]-$info[8]));
-        my $total1=$info[6];
-        my $total2=$info[13];
-        my $sd1=$info[3];
-        my $se1=$info[4];
-        my $sd2=$info[10];
-        my $se2=$info[11];
-        my $df=$total1+$total2-2;
-        my $tdist;
-        my $pval;
-        #TDIST, PVAL calculations with fail if standard dev, error, or counts are not real numbers
-        #or if 0 ends up in denominator
-        if ($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 $sd2==0){
-            ($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,$pval);
-        push (@all,\@info);
-    }
-}
-close CONV;
-
-#SORT THE HOMOLOGS BY THE SORTKEY OR BY DEFAULT DIFFERENCE IN MEAN FITNESSES
-if (!$sortkey){
-    $sortkey=14; #for mean difference
-}
-my @sorted = sort { $b->[$sortkey] <=> $a->[$sortkey] } @all;
-
-#FINISH THE HEADER BY ADDING COLUMN NAMES FOR MEAN-DIFF, DOF, TDIST, AND PVALUE
-my $field="MeanDiff(".$labels[0].'.'.$labels[1].")";
-push (@header,$field,"DOF","TDIST","PVALUE");
-
-#PRINT MATCHED HOMOLOG INFORMATION INTO A SINGLE OUTPUT FILE
-open OUT, '>',"$out";
-print OUT (join(',',@header),"\n");
-foreach (@sorted){
-    my @woo=@{$_};
-    print OUT join(',',@woo),"\n";
-    }
-
-close OUT;
-
-