#! /usr/bin/perl 

use strict;

#Scott Doniger
#January 19, 2005

#ReadTabDelimited.pl
#This is a simple program to read in a tab-delimited file (like what you
#might get out of Excel) and parse the different columns.
#You will hopefully see how file input and output works, and out to use arrays.

#To use the program enter perl ./ReadTabDelimited.pl filename
# where filename is a tab-delimited file

#You might also want to redirect the output using the greater than sign.

#perl ./ReadTabDelimited.pl file1 > newfile

#check out the contents of file1.

if (scalar (@ARGV) != 1){ #the phrase "scalar (@arrayname)" says "treat the array as a scalar", which in this case means
                          #the number of element in the array ARGV.
  die "You did not give me a file to work with. Please include the filename\n";
}

my $tabfile = shift @ARGV; #@ARGV is the array of the input parameters. Shift grabs the first parameter

open INPUT, $tabfile; #we're now creating a file handler called INPUT which will allow us to access the lines of $tabfile.

#Now we want to read through the file, put each column of the tab-delimited file into an array.
#For demonstration sake, we'll print out the first, third, and fifth columns.

my $counter = 0;
while (my $line = <INPUT>){ #so $line is now equal to the next line of the file
  my @data = split "\t", $line; #this line creates an array, @data. Each element of that array is a column of the line.
                                #split takes a delimiter (e.g. tab "\t", space "\s", comma ","), and a string. It returns
                                #each element of that string.

  print "line $counter = ".$data[0]."\t".$data[2]."\t".$data[4]."\n"; #print the line number, the first, third, and fifth element of the array.
  $counter++;
}

close INPUT;

#easy, right?