Re^2: Spltting Genbank File

First off, thanks for all the replies guys! I shouldn't have rushed my posting since I left out some much needed information so sorry about that.
Here is a sample entry in the genbank file. The biotype entry is after "/note". I thought I would have to do all lower case because a couple of the entries weren't uniform and had uppercase letters; is this not needed?

LOCUS       EU099432                 832 bp    DNA     linear   INV 27
+-APR-2009
DEFINITION  Bemisia tabaci strain 05-06 cytochrome oxidase subunit I-l
+ike (COI)
            gene, partial sequence; mitochondrial.
ACCESSION   EU099432
VERSION     EU099432.1  GI:158726330
KEYWORDS    .
SOURCE      mitochondrion Bemisia tabaci
  ORGANISM  Bemisia tabaci
            Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygo
+ta;
            Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aleyrod
+iformes;
            Aleyrodoidea; Aleyrodidae; Aleyrodinae; Bemisia.
REFERENCE   1  (bases 1 to 832)
  AUTHORS   Ma,W.H., Li,X.C., Dennehy,T.J., Lei,C.L., Wang,M., Degain,
+B.A. and
            Nichols,R.L.
  TITLE     Utility of MtCOI polymerase chain reaction-restriction fra
+gment
            length polymorphism in differentiating between Q and B whi
+tefly
            Bemisia tabaci biotypes
  JOURNAL   Insect Sci. 16 (2), 107-114 (2009)
REFERENCE   2  (bases 1 to 832)
  AUTHORS   Ma,W., Li,X., Degain,B. and Dennehy,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-AUG-2007) Entomology, The University of Ariz
+ona, 1140
            E. 4th St., Tucson, AZ 85721, USA
FEATURES             Location/Qualifiers
     source          1..832
                     /organism="Bemisia tabaci"
                     /organelle="mitochondrion"
                     /mol_type="genomic DNA"
                     /strain="05-06"
                     /db_xref="taxon:7038"
                     /country="USA: Arizona"
                     /note="biotype: B"
     gene            <1..>832
                     /gene="COI"
     misc_feature    <1..>832
                     /gene="COI"
                     /note="similar to cytochrome oxidase subunit I"
ORIGIN      
        1 atatgcatgg agtgattttt tggtccccca gaagtaatat ggcagattag tgcat
+tggac
       61 ttgatttgtt tggtcatcca taaggcaaaa ggcacaatag ggcttcgaag gttta
+ttgtt
      121 tgacgtcctc atatattcac agttggaata gatgtagata ctcgagctta tttca
+cttca
      181 gccactataa ttattgctgt tcccacagga attaaaattt ttagttggct tgcta
+ctttg
      241 ggtggaataa agtctaataa attaaggcct cttggccttt gatttacagg atttt
+tattt
      301 ttatttacta taggtgggtt aactggaatt attcttggta attcttctgt agatg
+tgtgt
      361 ctgcatgaca cttattttgt tgttgcacat tttcattatg ttttatcaat aggaa
+ttatt
      421 tttgctattg taggaggagt tatctattga tttccactaa tcttaggttt aacct
+taaat
      481 aattatagat tggtgtctca attttatatc atgtttattg gagtaaattt aactt
+ttttt
      541 cctcaccatt ttcttggttt agggggaatg cctcgtcgat attcagatta tgctg
+attgc
      601 tatctagtat gaaataaaat ttcttctgcg ggaaggattc tgagtattat ttctg
+ttatt
      661 tattttttat ttattgtttt agaatccttt cttcttctgc ggttagtaag attta
+agctt
      721 ggtgtaagta ggcatctaga atgaaagatt aataaaccag ctcttaatca cagtt
+ttaaa
      781 gagttgtgtt taactttttt tttctaatat ggcagattag ggccccggga aa
//
[download]

Here is my updated code that now contains more errors lol.

# Genbank Splitter
# Takes Accession number and biotype as name for new FASTA file
# Contents of new FASTA file is corresponding sequence

use strict;
use warnings;

$/ = "//";

# Constants
my $genfile = 'c:\bemisia_coi.gb';
my $outfile = "$accession_$biotype";
my ($OUT, $IN);

print "Input: $genfile\n";
open my $ifh, "<", $genfile or die "cannot open $genfile: $!\n";

while (my $chunk = <$ifh>){
   last if eof $ifh;
   $chunk = lc $chunk;
         my ($accession) = $chunk =~ /locus\s*([a-z]{8});
         my ($biotype) = $chunk =~ /biotype: ([a-z]{1});
         my ($sequence) = $chunk =~ "/origin(\*+)\/\/\";
            $sequence =~ s/\s|\d//g;
   my $outfile = "${accession}_${biotype}";

open my $ofh, '>' $outfile or die "cannot open $outfile: $!\n";

print "Printing to $outfile\n";

print $ofh, ">$accession $biotype\n^^\n$sequence";

close $ofh;

}
[download]

And here are the errors I get

C:\Users\Owner>perl c:\gen_split2.pl
Bareword found where operator expected at c:\gen_split2.pl line 22, ne
+ar "my ($b
iotype) = $chunk =~ /biotype"
  (Might be a runaway multi-line // string starting on line 21)
        (Do you need to predeclare my?)
Backslash found where operator expected at c:\gen_split2.pl line 22, n
+ear "bioty
pe\"
Unrecognized escape \s passed through at c:\gen_split2.pl line 23.
Unrecognized escape \d passed through at c:\gen_split2.pl line 23.
Scalar found where operator expected at c:\gen_split2.pl line 25, near
+ "my $outf
ile = "${accession}"
  (Might be a runaway multi-line "" string starting on line 23)
        (Do you need to predeclare my?)
Bareword found where operator expected at c:\gen_split2.pl line 25, ne
+ar "${acce
ssion}_"
        (Missing operator before _?)
String found where operator expected at c:\gen_split2.pl line 27, near
+ "open my
$ofh, '>' $outfile or die ""
  (Might be a runaway multi-line "" string starting on line 25)
        (Missing semicolon on previous line?)
Backslash found where operator expected at c:\gen_split2.pl line 27, n
+ear "$!\"
        (Missing operator before \?)
String found where operator expected at c:\gen_split2.pl line 29, near
+ "print ""

  (Might be a runaway multi-line "" string starting on line 27)
        (Missing semicolon on previous line?)
Bareword found where operator expected at c:\gen_split2.pl line 29, ne
+ar "print
"Printing"
        (Do you need to predeclare print?)
Backslash found where operator expected at c:\gen_split2.pl line 29, n
+ear "$outf
ile\"
        (Missing operator before \?)
String found where operator expected at c:\gen_split2.pl line 31, near
+ "print $o
fh, ""
  (Might be a runaway multi-line "" string starting on line 29)
        (Missing semicolon on previous line?)
Scalar found where operator expected at c:\gen_split2.pl line 31, near
+ "$accessi
on $biotype"
Global symbol "$accession_" requires explicit package name at c:\gen_s
+plit2.pl l
ine 12.
Global symbol "$biotype" requires explicit package name at c:\gen_spli
+t2.pl line
 12.
Global symbol "$biotype" requires explicit package name at c:\gen_spli
+t2.pl line
 21.
syntax error at c:\gen_split2.pl line 22, near "my ($biotype) = $chunk
+ =~ /bioty
pe"
Global symbol "$chunk" requires explicit package name at c:\gen_split2
+.pl line 2
3.
Global symbol "$sequence" requires explicit package name at c:\gen_spl
+it2.pl lin
e 23.
syntax error at c:\gen_split2.pl line 25, near "my $outfile = "${acces
+sion}"
Global symbol "$accession" requires explicit package name at c:\gen_sp
+lit2.pl li
ne 25.
Global symbol "$biotype" requires explicit package name at c:\gen_spli
+t2.pl line
 25.
Global symbol "$accession" requires explicit package name at c:\gen_sp
+lit2.pl li
ne 31.
c:\gen_split2.pl has too many errors.
[download]

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