[Bioperl-l] Bio/SeqIO/swiss.pm parsing error -

Chris Fields cjfields at uiuc.edu
Sun Nov 5 16:56:08 EST 2006


We'll try to get these in.  THe problem is we need to try and make  
this backwards compatible.  I'll post this as a bug for now as a  
reminder.

Chris

On Nov 3, 2006, at 2:56 PM, Erik wrote:

>
> I should have mentioned two more changes needed
> in Bio/SeqIO/swiss.pm for the new Swissprot
> format:
>
> In Bio/SeqIO/swiss.pm, next_seq():
> ===============
>   $params{'-namespace'} = ($2 eq 'Reviewed'   ) ? 'Swiss-Prot' :
>                           ($2 eq 'Unreviewed' ) ? 'TrEMBL'     :
>                        #  ($2 eq 'STANDARD'   ) ? 'Swiss-Prot' :
>                        #  ($2 eq 'PRELIMINARY') ? 'TrEMBL'     :
>                            $2;
> ===============
>
>
> and in Bio/SeqIO/swiss.pm, write_seq():
> ===============
>    $div = ($ns eq 'Swiss-Prot') ? 'Reviewed'    :
>           ($ns eq 'TrEMBL')     ? 'Unreviewed'  :
>        #  ($ns eq 'Swiss-Prot') ? 'STANDARD'    :
>        #  ($ns eq 'TrEMBL')     ? 'PRELIMINARY' :
>            $ns;
> ===============
>
> above, the old lines are shown as outcommented.
>
>
> again, hth,
>
> Erik
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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