Have you looked into Bioperl? It will simplify parsing for you (especially for the sequence itself). Here's a program that gets the sequence and some other basic information: 
#!/usr/local/bin/perl -w
use strict;

use Bio::SeqIO;

my $seqobj;

print "please type in the name of a file\n";
my $file = <STDIN>;

my $seqio  = Bio::SeqIO->new (-format => 'GenBank',
                              -file =>   $file);
while ($seqobj = $seqio->next_seq())
{
  printf "Sequence: %s\n",$seqobj->seq;

  # I'm not sure what you need other than the
  # sequence - here's some examples:
  printf "Display ID:  %s\n",$seqobj->display_id;
  printf "Description: %s\n",$seqobj->desc;
  printf "Division:    %s\n",$seqobj->division;
  printf "Accession:   %s\n",$seqobj->accession;
}

[download]
In your program, you're putting all of the non-sequence lines into @annotation. I'm not sure specifically which information you need (i.e. descriprtion, accession number, etc.), but those are all accessible through the "$seqobj" object. There's some examples in the code above; you'll find many more in the documentation.

This method also has the advantage of being able to handle multiple GenBank records per file.

This is just a tiny portion of the functions available with BioPerl - it will also parse BLAST files, perform alignments, etc. If you're interested, you can grab the latest release from CPAN or from BioPerl here. Hope this helps!

- robsv

In reply to Re: please help me!! by robsv
in thread please help me parse genbank DNA file by foxy

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.