#!/usr/bin/perl    
use strict;    
use warnings;    
use Bio::SeqIO;    
  
my $in  = Bio::SeqIO->new( -file   => "input.txt" ,    
                           -format => 'GenBank');    
  
open my $out, ">", 'fasta.out' or    
	die "Unable to open fasta.out for writing. $!";    
  
while ( my $seq = $in->next_seq() ) {    
	my @features = $seq->get_SeqFeatures(); # just top level    
	foreach my $feat ( @features ) {    
		next unless $feat->primary_tag eq 'CDS';    
       	print $out ">", $seq->desc, "\n";    
		print $out join("\n",    
			$seq->subseq(1 + $feat->end, $seq->length) =~ /.{1,60}/g), "\n";    
    }    
}    
close $out or die $!;    
  
  
__END__    
*** print out    
  
>Danio rerio cDNA clone MGC:198355 IMAGE:9039344, complete cds.    
GCGTTCATGGAGAAAACTTCACTCGTGGTCAAGACATGCCTGCTACCTGCATCCCCGAGC    
TCGGCCTTCAGTCACCAGGCTGCTCTGATCCCACCTGCGGTTTGCAGTTTACCAGAGGCT    
GTCCAAGGCAGTCTACCACAACCTGCGTGACATTAACACTGTCTGGTCTTAGCAGTAGTT    
GCAGTAGGAAGTCCCCCCCTTTCTCTGTCTTTAGGTTCTCACCTTCTGTTTTTGTAAATA    
ATGTTTGGCTCGCCAGCTTTA

#!/usr/bin/perl 
use strict; 
use warnings; 
use Bio::SeqIO; 
use 5.014; 
 
my $in  = Bio::SeqIO->new( -file   => "input.txt" , 
                           -format => 'GenBank'); 
my $out = Bio::SeqIO->new( -file   => '>fasta.dat', 
                           -format => 'fasta'); 
 
while ( my $seq = $in->next_seq() ) { 
	my @features = $seq->get_SeqFeatures(); # just top level 
	foreach my $feat ( @features ) { 
		next unless $feat->primary_tag eq 'CDS'; 
		my $subseq = $seq->trunc(1 + $feat->end, $seq->length); 
		$out->write_seq($subseq); 
    } 
} 
 
my $test = Bio::SeqIO->new( -file   => 'fasta.dat', 
                            -format => 'fasta'); 
 
while (my $seq = $test->next_seq()) { 
	say "ID"; 
	say	$seq->id, "\n"; 
	say "SEQ"; 
	say $seq->seq, "\n"; 
	say "DESC"; 
	say $seq->desc; 
} 
__END__ 
 
*** fasta.dat 
 
>BC171628 Danio rerio cDNA clone MGC:198355 IMAGE:9039344, complete cds. 
GCGTTCATGGAGAAAACTTCACTCGTGGTCAAGACATGCCTGCTACCTGCATCCCCGAGC 
TCGGCCTTCAGTCACCAGGCTGCTCTGATCCCACCTGCGGTTTGCAGTTTACCAGAGGCT 
GTCCAAGGCAGTCTACCACAACCTGCGTGACATTAACACTGTCTGGTCTTAGCAGTAGTT 
GCAGTAGGAAGTCCCCCCCTTTCTCTGTCTTTAGGTTCTCACCTTCTGTTTTTGTAAATA 
ATGTTTGGCTCGCCAGCTTTA 
 
*** test run 
 
C:\Old_Data\perlp>perl t5.pl 
ID 
BC171628 
 
SEQ 
GCGTTCATGGAGAAAACTTCACTCGTGGTCAAGACATGCCTGCTACCTGCATCCCCGAGCTCGGCCTTCAGTCACCAGGC 
TGCTCTGATCCCACCTGCGGTTTGCAGTTTACCAGAGGCTGTCCAAGGCAGTCTACCACAACCTGCGTGACATTAACACT 
GTCTGGTCTTAGCAGTAGTTGCAGTAGGAAGTCCCCCCCTTTCTCTGTCTTTAGGTTCTCACCTTCTGTTTTTGTAAATA 
ATGTTTGGCTCGCCAGCTTTA 
 
DESC 
Danio rerio cDNA clone MGC:198355 IMAGE:9039344, complete cds.