use strict;
use warnings;
use Getopt::Long;
use Bio::SeqIO;

### use perl /home/xiangyang/Chen_genome/perl_bin/extract_protein_dir.pl /home/xiangyang/Chen_genome/chen_gbk

my $path=$ARGV[0];
# my $filename=getcwd $path;
opendir DIR, $path or die $!;
my @dir = readdir DIR; 
closedir DIR;

foreach my $file(@dir){
     my $input="$path/$file";
     mkdir "$path/protein/";
     my $output="$path/protein/$file.pep";
    open(OUTPUT, ">$output");

#######################################################################################
my %options = (
#    input    => undef,
#    output   => undef,
     cdsCount => 0,
     dna      => 'F'
);
GetOptions(
    'i=s'   => \$options{'input'},

    'dna=s' => \$options{'dna'}
);
#######################################################################################
my $in = new Bio::SeqIO( -file => $input, -format => 'genbank' );
my $out = new Bio::SeqIO( -file => $output , -format => 'fasta' );


while ( my $seqObject = $in->next_seq() ) {
    my @features = $seqObject->get_SeqFeatures();
#--------------------------------------------------------------------------------------------display organism name for each CDS		
	my $org = "";
        foreach (@features) {
        my $feat = $_;
		my @ar;
		if ($feat->primary_tag() eq "source"){
				@ar = $feat->get_tag_values('organism');
				$org = $ar[0];
				# $org =~ s/\ /_/g;   addtion "_" among each word
			#	print STDERR "Found source tag: >$display<\n";
				next;
		}	
#---------------------------------------------------------------------------------------------xiangyang li addition 2013-01-25

       my $length = $seqObject->length();
       my $type = lc( $feat->primary_tag );
        unless ( $type eq "cds") {
            next;
        }
        my $start = $feat->start;
        my $stop  = $feat->end;

        my $location  = $feat->location;
        my $locString = $location->to_FTstring;
        my @loc       = split( /,/, $locString );

        if ( $loc[0] =~ m/(\d+)\.\.(\d+)/ ) {
            $start = $1;
        }

        if ( $loc[ scalar(@loc) - 1 ] =~ m/(\d+)\.\.(\d+)/ ) {
            $stop = $2;
        }

     
        

        my @label = ();
        if ( $feat->has_tag('locus_tag') ) {
                    push( @label, join( ",", $feat->get_tag_values('locus_tag') ) );
        }
        if ( $feat->has_tag('gene') ) {

            	#    push (@label, join(",",$feat->get_tag_values('gene')));
        }
        if ( $feat->has_tag('product') ) {

            	    push (@label, join(",",$feat->get_tag_values('product')));
        }

#-------------------------------------------------------------------------------------
            	    push (@label, join(",","[".$file."]"));
#-------------------------------------------------------------------------------------xiangyang li addition 2013-01-25

        if ( $feat->has_tag('function') ) {

                #    push (@label, join(",",$feat->get_tag_values('function')));
        }
         

        #add position information to label
        #label_start=4001;end=5000;strand=1;rf=1;
        #where strand is 1 or -1 and rf is 1,2, or 3
        #start should be smaller than the end
                #    push (@label, "_start=$start;end=$stop" );
        my $label = join( ";", @label );
        $label =~ s/\s+/_/g;
        $label =~ s/\n//g;
        $label =~ s/\t+/ /g;

        my $trans;
        if ( !( $feat->has_tag('translation') ) ) {
            print(
                "Warning: get_cds.pl was unable to obtain translation for $label. Skipping\n"
            );
            next;
        }
        else {
            my @translation = $feat->get_tag_values('translation');
            $trans = $translation[0];
            $trans =~ s/[^A-Z]//ig;
        }

    #    my $dna = $feat->spliced_seq->seq;
    #    if ( ( !( defined($dna) ) ) && ( $options{'dna'} =~ m/t/i ) ) {
    #        print(
     #           "Warning: get_cds.pl was unable to obtain the DNA coding sequence for $label. Skipping\n"
     #       );
     #       next;
     #   }
     #   $dna =~ s/[^A-Z]//ig;

        $options{cdsCount}++;
 

     #   if ( $options{'dna'} =~ m/t/i ) {
     #       print( OUTPUT "$label\n$dna\n\n" );
     #   }
     #   else {
            print OUTPUT ">$label\n$trans\n";
     #   }
    #    close(OUTPUT) or die("Cannot close file : $!");
 

    }

}
print    "A total of $options{cdsCount} records were written to $file.\n";
}