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

[Hilmar Lapp]

Where do you get this feature location from? This code is being tested 
with real records and passes; if this is an 'official' example it needs 
to be added to the tests to make sure we cope with it properly.

	-hilmar

On Friday, October 15, 2004, at 12:28  AM, Sang Chul Choi wrote:

> 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
>
> complement(join(2352..2759,2809..3015))
>
> 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();
>             }
>
> Thanks,
>
> Sang Chul
>
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>
-- 
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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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