[Bioperl-l] How to get sequence of joins

Henrik.Seidel@schering.de Henrik.Seidel@schering.de
Fri, 20 Oct 2000 11:43:28 +0200

Hi all,

I could not figure out a simple way to get the sequence of a CDS which looks

CDS complement(join(1..10,20..30)

The sequence member of the top level CDS_span object would be 1..30 and not the
join. Do I have to cycle through all the subfeatures of the top level CDS_span
and concatenate the sequences of all subfeatures which are a CDS_span as well,
or is there an easier way? Even if I concatenate them, how do I know that I have
to take the complement? In the top level CDS_span I did not find any field
containing or any member function returning an indication that this is supposed
to be the complement. Is there a function returning the correct sequence (i.e.,
after joining and taking the complement) of a top level CDS_span? Or is there a
function returning the complete original entry as it was in the source file
(i.e., "complement(join(1..10,20..30)")?

Any advice is appreciated.

Best regards