[Bioperl-l] Bioperl 1.4 to 1.5.2, adding qualifiers to Bio::Seq-objects

Chris Fields cjfields at uiuc.edu
Wed Feb 7 12:50:13 EST 2007


On Feb 7, 2007, at 11:11 AM, Adam Sjøgren wrote:

>   Hi.
>
>
> I am transitioning from Bioperl 1.4 to 1.5.2, and the qualifiers I add
> to features in Bio::Seq objects have stopped appearing when I output
> them as EMBL or GenBank-files.
>
> Below is a test-script that exercises the problem.
>
> I guess I should be doing something else when adding qualifiers, now
> with 1.5.2 (as reading an EMBL-file with Bio::SeqIO and outputting it
> again of course works perfectly), but I can't deduce what from perldoc
> Bio::SeqFeature::Generic - it still lists the add_tag_value method,
> and calling it doesn't croak nor warn.
>
> I have found some comments on this in the release notes of 1.5.0¹ on
> the Bioperl wiki, but I must admit I wasn't able to extract what
> methods I should be calling instead.
>
> If someone could point me to the relevant documentation or tell me
> what method to use instead, I would be happy as a clam.
>
>
>   Best regards,
>
>     Adam

...

This works for me using bioperl-live (Mac OS X):

ok 1 - Qualifier note found
ok 2 - Qualifier db_xref found

If I print the string I get:

ID   DB:D27; SV 1; linear; unassigned DNA; STD; UNC; 12 BP.
XX
AC   DB:D27;
XX
XX
FH   Key             Location/Qualifiers
FH
FT   source          2..8
FT                   /db_xref="DB:D27"
FT                   /note="TEST"
XX
SQ   Sequence 12 BP; 3 A; 3 C; 3 G; 3 T; 0 other;
      actgactgac  
tg                                                            12
//

GenBank also works:

LOCUS       D27                       12 bp    dna     linear   UNK
ACCESSION   DB:D27
FEATURES             Location/Qualifiers
      source          2..8
                      /db_xref="DB:D27"
                      /note="TEST"
BASE COUNT        3 a      3 c      3 g      3 t
ORIGIN
         1 actgactgac tg
//

If you haven't uninstalled 1.4, make sure you aren't running 1.4 or  
mixing the two versions (you can check by using 'perldoc -l  
Bio::Root::Root').

chris


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