fasta2nexus.pl

#!/usr/bin/perl

use strict;
use warnings;
use Getopt::Long;
use File::Path;
use File::Basename;

# Declare variables

my @input;
#our $infiletype=1;

parseArgs();

my ( $filepath, $dirpath ) = fileparse($input[0]);

#Iterate through files

@input = glob "@input";

foreach my $file ( @input ){

#Initialize variables within each daughter process
    my %data;
    my $taxa = 0;
    my @fasta;
    my @loci;
    my $nchar=0;
    my $line;
		my $name = "";
		my $seq = "";

    open ( FILE, "$file" ) || die "Error\nCan't open $file: $!\n";


	while ( <FILE> ){
			chomp;
			if( $_ =~ /^\>/ ){
				$taxa++;
				if ($name =~ ""){
					$_ =~ /^\>(\S+)/;
					$name = "$1";
				}else{
					$data{$name} = $seq;
					$seq = "";
					$nchar = length($seq);
					$_ =~ /^\>(\S+)/;
					$name = "$1";
				}
			}elsif( $_ =~ /^\s*$/ ){
				next;
			}elsif( $_ =~ /^\s*#/ ){
				next;
			}else{
				$seq .= $_; #append sequence to line; accounts for multi line fasta
			}
    }
    close FILE;

    #Capture taxa name to use as identifier
	my $filepath = fileparse("$file");
	$filepath =~ /(\w+)\.\w/;
	my $ID = $1;

    open( OUT, '>', "$dirpath$ID.nex" ) || die "Error\nCan't write to $ID.nex\n";
         print OUT "#NEXUS\n\n";
         print OUT "BEGIN DATA;
DIMENSIONS NTAX=$taxa NCHAR=$nchar;
FORMAT DATATYPE=DNA MISSING=? GAP=- ;

MATRIX\n";

	foreach my $key (keys %data){
		print OUT "$key\t$data{$key}\n";
	}
    print OUT ";\n";

    print OUT "END;\n\n";

    close OUT;
}


exit;
###########################SUBROUTINES###################################

sub parseArgs{
	#Message to print if mandatory variables not declared
	my $usage ="\nUsage: $0 --i /path/to/input/directory/*.fasta
Mandatory
	-i, --input	-  path to the input files in fasta format
\n";

	my $options = GetOptions
		(
		'input|i=s{1,}'		=>	\@input,
		);

	@input or die "\n\nError: Input not specified!\n\n$usage\n";
}

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