#!/usr/bin/perl

#Greetings by developer Rima Upchurch with help from James Henriksen. 
print "\n";
print "Welcome to PRELIBSHUFF, the formatting program for LIBSHUFF developed by Rima Ann Upchurch.\n";
print "Version 1.0 October 20, 2003\n";

#Specify the phylip file
print "What is the phylip file (For example mysequences.phy)? Reminder: You must be in the directory that this file is found.\n"; 
$phylipfile = <STDIN>;
chomp($phylipfile);

#Open file that has the aligned sequences
open (INFILE, "$phylipfile") || die "Unable to find file.\n";
@sequences = <INFILE>;
close (INFILE);

#Use match to find and s/ to substitute and search and replace ~ with -
foreach  $line(@sequences) 
	{
	$line =~ s/~/-/g;
	}

#Rewrite file to contain changes
print "Generating an infile for dnadist which will overwrite any file named infile in this directory.\n";
open (INFILE, ">infile");
foreach $line (@sequences)
	{
	print INFILE $line;
	}
close(INFILE);

#Now specify path to dnadist in Phylip package
print ("What is the path to DNADIST? (For example C:\\program files\\dnadist.exe) \n");
$phylip = <STDIN> || die "Unable to find DNADIST.\n";
chomp ($phylip);

#Run phylip dnaddist with added quotes to parse spaces in the path name
system ("\"$phylip\"");

#Formatting the outfile
#Put numbers into the array
open (OUTFILE, "< outfile") or die "no outfile\n";
@array = <OUTFILE>;
close (OUTFILE);

#Get rid of number at the top
splice (@array, 0, 1);

#Use match to find and s/ to substitute
foreach  $line(@array) 
{
#get rid of all new line characters
	$line =~ s/\n//g;
#substitute newline for words at the beginning
	if ($line =~ /^\S+/)
	{
		$line =~ s/^\S+\s+/\n/g;
	}
#substitute double space for tabs
	$line =~ s/  /\t/g;
}

#Opps there's one at the beginning we don't want
$array[0] =~ s/^\n//g;

#Save as sample file for libshuff 
print "Writing sample.txt to current directory, which will overwrite any file named sample.txt in this directory.\n";
open (SAMPLE, "> sample.txt") or die "no sample file found\n";
foreach $line (@array)
{
	print SAMPLE $line;
}
close (SAMPLE);