leosanbu

#!usr/bin/perl
#use strict;

my $path = $ARGV[0];                ## Argument: /path/to/file.xmfa ## MAUVE FORMAT ##
my $ref = $ARGV[1];                 ## Number of order of the sequence used as reference ##
my @path = split /\//, $path;
my $file = pop @path;
$path = join "\/", @path;

print "\nxmfa2fas\.pl\tversion 1.0\tLSB Oct2013\n\n";

leosanbu

## R functions ##

# Get GFF file #
get_GFF <- function(x){
  gff.tmp <- system(paste("less", x, "| grep \\\t"), intern=TRUE)
  gff.tmp <- strsplit(gff.tmp, "\t")
  gff.tmp <- do.call(rbind, gff.tmp)
}