[Bioperl-l] can't parse GenBank correctly (SeqIO or included modules)

[t-nakazato at muj.biglobe.ne.jp]

Hi,

I'll report the case that BioPerl can't parse GenBank file
correctly.
BioPerl (SeqIO or included modules) confuses REMARK and PUBMED
line in GenBank file.
I'm running Ver.1.5 on RedHat 9.


I wrote script as follows to retrieve PMID from GenBank file.

-----
#!/usr/bin/perl

use Bio::SeqIO;

my $file_in = shift;

my $in_obj  = Bio::SeqIO->new( -file   => "$file_in",
                               -format => "GenBank" );

while ( my $each_obj = $in_obj->next_seq) {
    @ref_objarray = $each_obj->annotation->get_Annotations("reference");

    foreach $ref_obj (@ref_objarray) {
        print $ref_obj->pubmed();
    }
}
-----

Most of GenBank file is parsed correctly, but I can't get PMID
from AC091629 or AC002397 (GenBank Accession No.).  (Nothing is
printed.)


Original GenBank file is as follows.
(in the case of AC091629)

-----
...
REFERENCE   1  (bases 1 to 161334)
  AUTHORS   Poorkaj,P., Kas,A., D'Souza,I., Zhou,Y., Pham,Q., Stone,M.,
            Olson,M.V. and Schellenberg,G.D.
  TITLE     A genomic sequence analysis of the mouse and human
            microtubule-associated protein tau
  JOURNAL   Mamm. Genome 12 (9), 700-712 (2001)
  REMARK    Contact: Gerald D. Schellenberg (zachdad at u.washington.edu)
   PUBMED   11641718
...
-----


So, I'll try "print $ref_obj->comment();".

-----
Contact: Gerald D. Schellenberg (zachdad at u.washington.edu) PUBMED   11641718
-----

I checked BioPerl confuses "comment" and "pubmed" in $each_obj
(in my script, SeqIO object) with Data::Dumper.


Ver.1.4 confuses JOURNAL and PUBMED line.
This problem was fixed in 1.5, but it seems to remain.


Best regards,
Takeru