[Bioperl-l] Problem in parsing GenBank flatfile

[Brian Osborne]

Yoshida,

Whatever the problem is it appears to be fixed in bioperl-live, in CVS. I
downloaded the most recent NT_015926 and it's parsed correctly.

Brian O.



On 6/9/05 5:39 AM, "Yoshida Yuichi" <yuichiyoshi at gmail.com> wrote:

> Dear all,
> 
> I am trying to parse GenBank flatfile (accession num is NT_015926)
> by calling Bio::SeqIO modules, but I can not.
> 
> - - - - - - - - - - - - - Perl program code - - - - - - - - - - - - -
> #!/usr/bin/perl
> use Bio::SeqIO;
> 
> $gbk_filename = shift @ARGV;
> $seqin = Bio::SeqIO->new(-file=>$gbk_filename, -format=>'Genbank');
> 
> while ($seqobj = $seqin->next_seq) {
>     $accession = $seqobj->accession_number,"\n";
>     foreach my $feat ($seqobj->get_SeqFeatures()){
>         if ($feat->primary_tag eq 'mRNA'){
>             $db_gene_name = join(' ',$feat->get_tag_values('gene'));
>             $db_transcript_id = join('
> ',$feat->get_tag_values('transcript_id'));
>             $start = $feat->start; $end = $feat->end;
>             print $db_transcript_id,"\t",$db_gene_name,"\t",$accession,"\t";
>             print $start,"\t",$end,"\n";
>         }
>     }
> }
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> 
> The following error message is shown.
> 
> - - - - - - - - - - - - - error message - - - - - - - - - - - - -
> -------------------- WARNING ---------------------
> MSG: cannot see new qualifier in feature CDS: aa:OTHER)
> ---------------------------------------------------
> 
> -------------------- WARNING ---------------------
> MSG: cannot see new qualifier in feature CDS: aa:OTHER)
> ---------------------------------------------------
> 
> -------------------- WARNING ---------------------
> MSG: cannot see new qualifier in feature CDS: aa:OTHER)
> ---------------------------------------------------
> out of memory
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> 
> The parts which cause the error (I guess) is shown as the followings.
> 
> - - - - - GenBank partial flatfile (NT_015926) - - - - -
>      CDS             complement(join(4528741..4528932,4543408..4543490,
>                      4581809..4582043,4616648..4616817,4632093..4632236,
>                      4643148..4643301))
>                      /gene="FLJ21820"
>                      /note="go_function: catalytic activity [goid 0003824]
>                      [evidence IEA];
>                      go_process: lipid metabolism [goid 0006629] [evidence
>                      IEA]"
>                      /codon_start=1
>                      /product="hypothetical protein FLJ21820"
>                      /protein_id="NP_068744.1"
>                      /db_xref="GI:11345458"
>                      /db_xref="GeneID:60526"
>                      /db_xref="LocusID:60526"
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> 
> Would you please tell me the way to solve this problem?
> 
> --
> Yuichi Yoshida <yuichiyoshi at gmail.com>
> 
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