[Bioperl-l] Bio::SeqIO::genbank seems to munge SOURCE and ORGANISM lines

[Hilmar Lapp]

Can you submit this as bug report to http://bugzilla.bioperl.org/?

Thanks,

	-hilmar

On Friday, February 21, 2003, at 04:53  AM, Geoff Purdy wrote:

> I've noticed some more strange behavior with reading
> and printing GenBank files using Bio::SeqIO.
>
> It appears that the SOURCE and ORGANISM lines are
> being corrupted by BioPerl in some records.  Below is
> an example using GenBank accession AE016800 (for ease
> of reading, I've removed the uneffected surounding
> lines):
>
>> From the original genbank file:
> SOURCE      Vibrio vulnificus CMCP6
>   ORGANISM  Vibrio vulnificus CMCP6
>
>
>> From the output after reading in an printing out with
> Bio::SeqIO:
> SOURCE      Vibrio vulnificus CMCP6 CMCP6.
>   ORGANISM  Vibrio vulnificus
>
> You can see that CMCP6 was dropped from the ORGANISM
> and appended (along with a mystery period) to the
> SOURCE.
>
> Is this a known issue, or should I submit it to
> bugzilla?
>
> Here is the code snippet that I used for reading the
> file and writing it back out:
>
> my $in  = Bio::SeqIO->newFh(-file => "AE016800.gb" ,
>                             '-format' => 'Genbank');
>
> my $out = Bio::SeqIO->newFh('-format' => 'Genbank');
>
> print $out $_ while <$in>;
>
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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