#!/usr/bin/perl 
 
use strict; 
use warnings; 
 
sub ReadFile{ 
 
	my $infile = $_[0]; my $hash_string = $_[1]; 
 
	open (INFILE , "<$infile") or die ("Cannot open infile fasta: $infile. $!\n"); 
		my $string = ""; 
		my @strings; 
 
        while (my $line = <INFILE>) { 
        	chomp ($line); 
			if ($line =~ m/LOCUS/){ 
                	   $string = $line; 
			   push (@strings, $string); 
			   $hash_string -> {$string} = "$line\n"; 
			} 
                        else { 
                           $hash_string -> {$string} .= $line; 
			} 
        } 
	close INFILE; 
    	return; 
} 
 
 
sub FindSpecies { 
 
	my $hash_string = $_[0]; my $outfile = $_[1];  
 
	open (OUTFILE , ">$outfile") or die ("Cannot open outfile fasta: $outfile. $!\n"); 
 
		foreach my $line (keys %$hash_string) { 
			if ($line =~ m/ORGANISM/){ 
			  if (my $sp =~ (/((.+)\n(.+)\;(.+)\;(.+)(.+))/)) { 
            			 $sp = $5; my $string = "";                
                                if ($sp =~ m/Equinodermata/){ 
				   print OUTFILE "$hash_string->{$string}\n"; 
				 } 
			  } 
			} 
		} 
	close OUTFILE; 
	return; 
} 
 
my $infile = $ARGV[0]; 
my %hash_string = (); 
my $outfile = $infile.".final"; 
 
 
ReadFile ($infile, \%hash_string); 
FindSpecies (\%hash_string, $outfile);

open (OUTFILE , ">$outfile") or die ("Cannot open outfile fasta: $outfile. $!\n");

#change this 
open (INFILE , "<$infile") or die ("Cannot open infile fasta: $infile. $!\n");  
#to this 
open (INFILE , "$infile") or die ("Cannot open infile fasta: $infile. $!\n");  
 
#change this 
open (OUTFILE , ">$outfile") or die ("Cannot open outfile fasta: $outfile. $!\n");  
#to this (>> is append mode) 
open (OUTFILE , ">>$outfile") or die ("Cannot open outfile fasta: $outfile. $!\n");

#!/usr/bin/perl 
 
use strict; 
use warnings; 
use Bio::GenBankParser; 
use Data::Dumper; 
 
my $parser = Bio::GenBankParser->new( file => 'sequence.gb'); 
 
while ( my $seq = $parser->next_seq ) { 
    print Dumper $seq; 
}

[rkb@099-91-RKB01 ~]$ ./genbank.pl  
 
     ERROR (line 131): Invalid section: Was expecting commented line, or 
                       header, or locus, or dbsource, or definition, or 
                       accession line, or project line, or version line, or 
                       keywords, or source line, or organism, or reference, or 
                       features, or base count, or contig, or origin, or 
                       comment, or record delimiter 
 
 
     ERROR (line 131): Invalid startrule: Was expecting eofile but found 
                       "PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN 
                       COMP" instead