#!/usr/bin/perl -w
#
# Documentation of program in pod format
#
=pod

=head1 Perl template. Fasta splitter

Revision History
$Log: template.pl,v $
Revision 1.3  2002/03/05 13:23:45  lund
Revision history added


=cut
#
# Import libraries
#
use Getopt::Std;			# Command line options
use File::Path;				# mkpath, rmtree commands
use strict;				# Strict parsing
use English;				# Allow use of long names (Camel p. 127)
use lib "$ENV{VACHOME}/lib/perl";	# Path to perl modules
#
# Get command line options. Each command line option must be present in the
# Use vars line and in the getoptys line. colon after an option means that it
# takes an argument.
#

use vars qw($opt_h $opt_o $opt_f); #### Declaration of the variables where the options are stored
getopts('hf:o:')||usage();         #### Options taken from commandline with preceding - 
                                   ####    Colon (:) after an option means that a value is read off the commandline
                                   ####    No colon means that the option is an off/on switch
#
# usage prints a description of how to use the program
#
sub usage{
  print("Usage: $0 \[-h\] \[-o outputfile\] \[-f definition_file\] [inputfile(s)]\n");
  print("If no inputfiles are given data is read from standard in\n");
  print("Command line options:\n");
  print("	h: Print this meassage\n");
  print("	f: File to read extra stuff from\n");
  print("	o: Write to output file. Default is standard out\n");
  exit;
}
#
# If -h option is used, print description of usage
#
if (defined($opt_h)) {usage()};
#
# Open outputfile or write to std out
#
if (not defined($opt_o)) {$opt_o="-";} ### if no -o is set on the commandline $opt_o contains the string "-";
open(OUT, ">$opt_o") or die "Can't open $opt_o for writing: $!"; ### If a file with the name $opt_o cannot be opened
                                                                 ### the program dies with an error message
                                                                 ### $! contains error messages from the system
#
# Open xtra input file ()
#
if (defined($opt_f)) {
  open(IN, "<$opt_f") or die "Can't open $opt_f for reading: $!";
}

################################################################################
#
# Parse input
#
################################################################################
#

my @fields;       ########## Declaration of an array
my @words;        ########## Another array
my $var;          ########## Declaration of a variable;

while(<STDIN>){                     #### Reads the current line of the file
  print "$_";                       #### print the default input variable to stdout
}

if(defined($opt_f)){                #### If an input file is defined on the commandline

  while(!eof(IN)){                  #### Continue until the end of the file

    $var=<IN>;                      #### Transfer the content of the current line to
                                    #### the variable $var and shift to the next line
                                    #### of the file
    $_=$var;

    @fields = split;                #### Split the default input variable $_ on one or more
                                    #### whitespaces but ignores any preceeding whitespaces

    @words=split/\s/,$var;          #### Split the variable $var on one or more
                                    #### whitespaces including any preceeding whitespaces


    foreach my $oneword (@fields){  #### The content of each defined position in the array
                                    #### is transfered to the variable just declared

      printf OUT "%s ", $oneword ;  #### Print the variable $oneword to the file OUT
    }
    printf OUT "%s", $_;            #### Print the variable $_ (i.e. the whole line) to the file OUT
    
  
    foreach my $aword (@words){   #### The content of each defined position in the array
                                    #### is transfered to the variable just declared

      
      printf OUT "%s ", $aword ;  #### Print the variable $oneword to the file OUT
    }
    printf OUT "%s", $_;            #### Print the variable $_ (i.e. the whole line) to the file OUT
  }
}



my $cmd ="echo \"Ho Ho\nHa Ha\n\""; 
system("$cmd");                     #### Run the echo command (could be any executable)

open(HO, "$cmd |");                 #### Run the echo command (could be any executable)
                                    #### and pipe it to the filehandle
                                    #### Works as if the output of the command was written 
                                    #### to a file, and the file then opened for reading.


my @lines=<HO>;                     #### Read all lines from the files and transfer
                                    #### those the array (one line per place starting at 0)
close(HO);                          #### Close the file


for(my $n=0; $n<scalar(@lines); $n++){    #### As long as $n is lower than the number of
                                          #### places in the array

  $var=$lines[$n];                        #### Copy the content of line number $n to $var
  chomp($var);                            #### Remove the \n from $var
  for(my $i=0; $i<length($var)-1; $i++){  #### As long as $i is lower than the number of characters in $var

    printf STDERR "%s\n", substr($var,$i,2); #### Print to stderr to consecutive characters
                                             #### from $var starting at position $i (first pos is 0)
  } 
}
    

################################################################################
#
# Close outputfile and inputfile
#
################################################################################
#
# Close outputfile
#
close(OUT);
#
# Close inputfile if opened
#
if(defined($opt_f)){
  close(IN);
}
#
################################################################################
#
# End of program
#
################################################################################