--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compStrains.pl	Wed Mar 29 18:04:58 2017 -0400
@@ -0,0 +1,175 @@
+#!/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
+
+
+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
+);
+
+
+#THE @files ARRAY WILL CONTAIN INPUT FILE NAMES
+my @files=($input1,$input2);
+
+#GET LABELS:
+my @labels = ($l1,$l2);
+
+sub cleaner{
+    my $line=$_[0];
+    chomp($line);
+    $line =~ s/\x0d{0,1}\x0a{0,1}\Z//s;
+    return $line;
+}
+
+
+#CHECK IF REQ. VARIABLES WERE DEFINED USING FLAGS. IF NOT THEN USE DEFAULT VALUES
+if (!$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]; #get rid of blank columns
+for (my $j=0;$j<scalar @cols;$j++){
+    $cols[$j]=cleaner($cols[$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 6 columns (Ones about blanks aren't needed for comparisons)
+    @info=@info[0,1,2,3,4,5];
+    #Sometimes genes that don't have a gene name can't be blank, so fill with NA
+    if (!$info[5]){
+        $info[5]="";
+    }
+
+    $one{$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]; #get rid of blank columns
+for (my $j=0;$j<scalar @cols;$j++){
+    $cols[$j]=cleaner($cols[$j]).'-'.$labels[1];   #mark each column name with file it comes from
+}
+push (@header,@cols);
+
+while (my $line=<F2>){
+    $line = cleaner($line);
+    my @info=split(",",$line);
+    @info=@info[0,1,2,3,4,5];
+    if (!$info[5]){
+        $info[5]="";
+    }
+
+    $two{$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>){
+    $line = cleaner($line);
+    my @genes=split("\t",$line);   #Array @genes will contain two genes (SP_0000,SPT_0000)
+    if (scalar @genes==2 and (exists $one{$genes[0]}) and (exists $two{$genes[1]})){
+        my @info;
+        my @oneArray=@{$one{$genes[0]}};
+        my @twoArray=@{$two{$genes[1]}};
+        push (@info,@oneArray,@twoArray);
+        # Fitness values at index 1 and 7
+        my $diff=sprintf("$round",($info[1]-$info[7]));
+        my $total1=$info[2];
+        my $total2=$info[8];
+        if (!$info[3] or $info[3] eq ""){$info[3]="NA"};
+        if (!$info[4] or $info[4] eq ""){$info[4]="NA"};
+        if (!$info[9] or $info[9] eq ""){$info[9]="NA"};
+        if (!$info[10] or $info[10] eq ""){$info[10]="NA"};
+        my $sd1=$info[3];
+        my $se1=$info[4];
+        my $sd2=$info[9];
+        my $se2=$info[10];
+        my $df=$total1+$total2-2;
+        my ($tdist,$pval);
+        #TDIST, PVAL calculations with fail if standard dev, error, or counts are not real numbers
+        #or if 0 ends up in denominator
+        if ($sd1 eq "NA" or $sd2 eq "NA" 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=12; #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, '>',"$out";
+print OUT (join(',',@header),"\n");
+foreach (@sorted){
+    my @comparison=@{$_};
+    print OUT join(',',@comparison),"\n";
+    }
+
+close OUT;
+
+