[Bioperl-l] It seems a bug: Bio/SeqFeatureI.pm?

Sang Chul Choi goshng at naver.com
Fri Oct 15 00:28:45 EDT 2004

Dear Friends:

In the file Bio/SeqFeatureI.pm, there seems a small bug which should be fixed.
I tried to used the method of Seq Object called spliced_seq(). But, when I
have Bioperl parse the line like 


It just complements each fragment and then joins them together. And, I have
a strange translated protein. So, I changed the order of operation, and
it works.

            # This is dumb, subseq should work on locations...
            if( $loc->strand == 1 ) {
                $seqstr .= $called_seq->subseq($loc->start,$loc->end);
            } else {
                #$seqstr = $called_seq->trunc($loc->start,$loc->end)->revcom->seq() . $seqstr;
                $seqstr .= $called_seq->trunc($loc->start,$loc->end)->revcom->seq();


Sang Chul

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