[Bioperl-l] Parsing join(x1..x2,x3..x4)!

[Hilmar Lapp]

Johan, can you provide the sequence in question (e.g. by accession), 
and the output your piece of code produces?

Also, I presume you're using version 1.0.2 or higher. If not, please 
upgrade and let us know if the problem persists.

	-hilmar

On Wednesday, October 23, 2002, at 01:57 AM, Johan Geijer wrote:

> Hello!
>
> I'm having problems to parse the join shown below using the code shown
> below.  It's possible to collect both of the starts and stops but it's
> not possible to collect the note.. Does anyone know why..  Solution??
>
>
>  Piece of Genbak record I want to extract....
>
>  misc_feature    join(1511..11036,13779..20629)
>                            /note="regions of repeated incomplete
> cruzipain ORFs;
>                                         probably pseudogenes"
>
>
>
> A piece of the code I'm using...
>
> use Bio::Seq;
> use Bio::SeqIO;
> use Bio::SeqFeatureI;
>
> foreach $feat ( $seq->all_SeqFeatures() )
>    {
>      if($feat->primary_tag eq "misc_feature")
>         {
>            print FASTAOUT " ", $feat->start," ",$feat->end ,"
> ",$feat->strand," ","\n";
>            if($feat->has_tag('note'))
>              {
>                 @note = $feat->each_tag_value('note') ;
>                 print FASTAOUT "  ", $note[0], " ";
>               }
>          }
>     }
>
> Regards
>
> Johan
>
>      #####################################
>>  Johan Geijer
>>  Center for Genomics and Bioinformatics
>>  Karolinska Institutet
>>  Berzelius väg 37
>>  171 77 Stockholm, SWEDEN
>>  E-mail: Johan.Geijer@cgb.ki.se
>> #####################################
>> _________________________________________
>
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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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