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

Erik er at xs4all.nl
Fri Nov 3 15:56:47 EST 2006


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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