root/bin/fix_fasta

#! /usr/bin/perl
use strict;
use FindBin;
use lib "$FindBin::Bin/../lib";
use lib "$FindBin::Bin/../perl/lib";
use Fasta;
use Iterator::Fasta;
use File::Temp qw(tempfile);

my $file = shift;

if(! $file){
    exit;
}

#set up names and variables
my $fasta_iterator = new Iterator::Fasta($file);

#write fastas here
my ($FA, $t_full) = tempfile;
while (my $fasta = $fasta_iterator->nextEntry()) {
    my $def = Fasta::getDef(\$fasta);
    my $seq_ref = Fasta::getSeqRef(\$fasta);

    #fix non standard peptides
    $$seq_ref =~ s/\*//g;
    $$seq_ref =~ s/[^abcdefghiklmnpqrstvwyzxABCDEFGHIKLMNPQRSTVWYZX\-\n]/C/g;

    #Skip empty fasta entries
    next if($$seq_ref eq '');
    
    #reformat fasta, just incase
    my $fasta_ref = Fasta::toFastaRef($def, $seq_ref);
    
    #build full file
    print $FA $$fasta_ref;
}
close($FA); #close full file

#move finished files into place
system("mv $t_full $file");