LOCUS       EU099432                 832 bp    DNA     linear   INV 27-APR-2009
DEFINITION  Bemisia tabaci strain 05-06 cytochrome oxidase subunit I-like (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; Pterygota;
            Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aleyrodiformes;
            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 fragment
            length polymorphism in differentiating between Q and B whitefly
            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 Arizona, 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 tgcattggac
       61 ttgatttgtt tggtcatcca taaggcaaaa ggcacaatag ggcttcgaag gtttattgtt
      121 tgacgtcctc atatattcac agttggaata gatgtagata ctcgagctta tttcacttca
      181 gccactataa ttattgctgt tcccacagga attaaaattt ttagttggct tgctactttg
      241 ggtggaataa agtctaataa attaaggcct cttggccttt gatttacagg atttttattt
      301 ttatttacta taggtgggtt aactggaatt attcttggta attcttctgt agatgtgtgt
      361 ctgcatgaca cttattttgt tgttgcacat tttcattatg ttttatcaat aggaattatt
      421 tttgctattg taggaggagt tatctattga tttccactaa tcttaggttt aaccttaaat
      481 aattatagat tggtgtctca attttatatc atgtttattg gagtaaattt aacttttttt
      541 cctcaccatt ttcttggttt agggggaatg cctcgtcgat attcagatta tgctgattgc
      601 tatctagtat gaaataaaat ttcttctgcg ggaaggattc tgagtattat ttctgttatt
      661 tattttttat ttattgtttt agaatccttt cttcttctgc ggttagtaag atttaagctt
      721 ggtgtaagta ggcatctaga atgaaagatt aataaaccag ctcttaatca cagttttaaa
      781 gagttgtgtt taactttttt tttctaatat ggcagattag ggccccggga aa
//

##</code><code>##

# 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;

}

##</code><code>##

C:\Users\Owner>perl c:\gen_split2.pl
Bareword found where operator expected at c:\gen_split2.pl line 22, near "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, near "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, near "${acce
ssion}_"
        (Missing operator before _?)
String found where operator expected at c:\gen_split2.pl line 27, near "open my
$ofh, '>' $outfile or die ""
  (Might be a runaway multi-line "" string starting on line 25)
        (Missing semicolon on previous line?)
Backslash found where operator expected at c:\gen_split2.pl line 27, near "$!\"
        (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, near "print
"Printing"
        (Do you need to predeclare print?)
Backslash found where operator expected at c:\gen_split2.pl line 29, near "$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_split2.pl l
ine 12.
Global symbol "$biotype" requires explicit package name at c:\gen_split2.pl line
 12.
Global symbol "$biotype" requires explicit package name at c:\gen_split2.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_split2.pl lin
e 23.
syntax error at c:\gen_split2.pl line 25, near "my $outfile = "${accession}"
Global symbol "$accession" requires explicit package name at c:\gen_split2.pl li
ne 25.
Global symbol "$biotype" requires explicit package name at c:\gen_split2.pl line
 25.
Global symbol "$accession" requires explicit package name at c:\gen_split2.pl li
ne 31.
c:\gen_split2.pl has too many errors.