[Bioperl-l] Bug in SeqIO genbank output

[Heikki Lehvaslaiho]

Wes,

You didnot say which versionof bioperl you are using. For some reason which I 
can not quite understand, the current code:
          $self->_print(sprintf("%-6s%s\n",'ORIGIN',$o ? $o->value : ''));

does print out the requred six spaces after the word ORIGIN. This was recently 
fixed. Now, why doesn't it work for you? Could you check that you do not have 
multiple copies of bioperl in your computer and the older one gets accidently 
executed?

Sorry, I can not comeupwith any better explanation,

	-Heikki

On Tuesday 16 Dec 2003 4:38 am, Wes Barris wrote:
> Hi,
>
> I have just succeeded in tracking down a bug that prevents genbank files
> written from bioperl from being properly imported into StackPack
> (clustering software).  The problem is due to a subtle difference in
> a genbank entry downloaded from NCBI and a genbank entry produced using
> genbank.pm.  If you use "od -c" to look at a genbank record from NCBI,
> you will notice that the word "ORIGIN" is followed by six space characters.
>
> ORIGIN
>          1 cggccgcgtc gacttttttt ttaggtattt ttctcttatt atttctaaaa
> tataaatttt 61 ggacattcaa aagtgcaaca ngttaatgtg cctgtgggga atatcacagt
> taaaaaaata
>
> If I process this file using bioperl and then write out a new genbank
> format file, the word "ORIGIN" is followed immediately by a carriage return
> (newline) character.
>
> It seems silly to me that spaces should be required after the word
> "ORIGIN", but they do exist in files downloaded from NCBI and StackPack
> seems to require these space characters in order to import a genbank file. 
> Is there an official specification for the genbank format?  I have sent a
> bug report to the makers of StackPack too.
>
> In the meantime, I have modified my installed copy of Bio/SeqIO/genbank.pm
> changing this line:
>
>          $self->_print(sprintf("%-6s%s\n",'ORIGIN',$o ? $o->value : ''));
>
> to this:
>
>          $self->_print(sprintf("%-12s%s\n",'ORIGIN      ',$o ? $o->value :
> ''));

-- 
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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
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