process some sequences for CEGMA processing

cegma_format.pl

#!env perl
use strict;
use warnings;

my $dir = shift || "marker_files";
my $odir = shift || "marker_hmm";
mkdir($odir) unless -d $odir;
opendir(DIR,$dir)|| die "cannot open $dir: $!";
my $locusct =1;
for my $file ( readdir(DIR) ) {
    next unless $file =~ /(\S+)\.fa$/;
    my $gene = $1;
    open(my $in => "$dir/$file") || die $!;
    # make the AFTOL gene name just sequentially going through this
    my $aftolname = sprintf("AFTOL%03d",$locusct++);
    open(my $out => ">$odir/$gene.fa") || die $!; 
    while(<$in> ) { 
	s/^>([^\|]+)\|/>/; # get rid of the leading 'species prefix' 
	                   # >SPECIES|GENE
	s/^>(\S+)/>$1\_\_$aftolname/; # rename to LOCUS_AFTOL123
	s/\*//g; # stop codons from AA file, muscle and hmmer don't like these
	print $out $_; # just print back out the line to the open filehandle
    }
}