work in progress...

tableJoin.pl

#!/usr/bin/perl

use strict;
#use warnings;

require "getopts.pl";
   
use vars qw ($opt_f $opt_s $opt_h $opt_H);

&Getopts('f:s:hH:');
my $executable = "transposer.pl";
$| = 1;
my $usage = qq{
    
  ###################################################################
  usage:  $executable -f fileName
          used for transposing a table (rows to columns and columns to rows)

	  # -f the file name; will use stdin if specified as "stdin".
          #  
          # -s column separator
          #    [default: tab]
          #    C: comma
          #    S: space   
          #
	  # -hH print this 
	example: >$executable -f testInputFile -s S > output

 ####################################################################
	\n};
my ($inputFile, $separator, $FILE);
# options:
if (length($opt_h) > 0 || length($opt_H) > 0 ) {die($usage);}
if (-s $opt_f) {$inputFile = $opt_f; } 
elsif ($opt_f =~ /stdin/i) {$inputFile = "stdin"; }
else {die("Error: must have a input file for -f $opt_f !!!\n$usage"); }
#if ($opt_s =~ /^C/i ) {$separator = "comma";  }elsif ($opt_s =~ /^S/i) {$separator = "space"; } else {$separator = "tab"; }

#interpretation of user input for delimiters (comma, space, or tab[default])
if ($opt_s =~ /^C/i ) {$separator = ",";  }elsif ($opt_s =~ /^S/i) {$separator = " "; } else {$separator = "\t"; }

#establish scalar variables for lines, columns, etc. Columns are stored as an array because they will be printed
#as lines in the final product. A hash of data is stored so that column numbers act as keys for line numbers. 
my ($line, $lineNo, $colNo, $colData, @cols, %data);

#The || or option here produces an error when the user does not have appropriate permissions to open the file.
if ($inputFile =~ /\.gz$/i) { 
    open ($FILE, "zcat $inputFile |" ) || die ("Error:cannot open the input file $inputFile specified by -f !!!");
}elsif ($inputFile eq "stdin") {
    $FILE = \*STDIN;
}else {
    open ($FILE, $inputFile) || die ("Error:cannot open the input file $inputFile specified by -f !!!");
}

#This loop determines columns by using a separator given by the user, line by line.
while(<$FILE>) {
    chomp; #This removes the newline from analysis
    $line = $_; #Store the temporary value of $_ to $line
    $lineNo++; #Analyze each line in ascending order (as in 0,1,2...n)
    #The following separates strings found in each line and 
    #transfers these scalars in the array called @cols (columns).
    @cols = split (/$separator/, $line);
    $colNo = 0; #start from colNo0
    #This loop ties together data from $colNo and $lineNo into the %data hash. Because they are switched upon
    #assignment to $colData, the rows will become columns. 
    foreach $colData (@cols) { #perform operation on each $colData found in the array @cols
	$colNo++; #go up each value starting from 0 (as specified above)
	$data{$colNo}{$lineNo} = $colData;
    }    
}
close ($FILE);

#$transposedLine gets concatenated via ".=" to the tab-separated content of $colData.
my $transposedLine; 
foreach $colNo (sort {$a<=>$b} keys %data) { # $a<=>$b specifies that data is sorted numerically
    $transposedLine = ""; #establishes an empty string for $transposedLine
    #This loop sorts the data stored in $colNo numerically.
    foreach $lineNo (sort {$a<=>$b} keys %{$data{$colNo} } ) { #again data is sorted from smallest to largest according to the hash of %data
	$colData = $data{$colNo}{$lineNo}; #i becomes j, j becomes i
	$transposedLine .= "$colData\t"; #concatenates the empty string to tab-separated $colData
    }
    $transposedLine =~ s/\t$//; # Tabs found at the end of a line are replaced with nothing. 
    print "$transposedLine\n"; #print the final product
}

#Now we exit!
exit;

#Okay, so the goal is to merge two tables together, and give users the option to merge everything or just the 
#rows/columns that match between the two tables.

#To open and cat two files:
#@ARGV = ('file2.txt', 'file4.txt', 'file15.txt');

#open SEL, '>', 'selected.txt' or die $!;

#while (<>) {
#  print SEL;
#}