PrimarySeqI.pm patch [was Re: [Bioperl-l] Copying features]

[Heikki Lehvaslaiho]

Rob,

Looks good. It should go into Bio::SeqI, though. PrimarySeqs do not know
about features. Could you write a test code for this into t/Seq.t,
please.

	-Heikki


On Sun, 2003-05-11 at 18:08, Rob Edwards wrote:
> Marc's suggestion works well for duplicating a feature and is easy :) Thanks.
> 
> It seems to me that a reverse complemented sequence should still retain its 
> features. 
> 
> I'd like to propose the following patch to PrimarySeqI.pm that will put new 
> features on a reverse complemented sequence.
> 
> Rob
> 
> diff PrimarySeqI.pm PrimarySeqI_original.pm
> 424,440d423
> <     foreach my $feature ($self->get_SeqFeatures) {
> <        # here we are going to make a copy of the SeqFeature to put on the 
> new
> <        # sequence. This code was suggested by  Marc Logghe 
> <Marc.Logghe at devgen.com>
> <        # This way, the original feature is not altered.
> <        # $rf is reverse feature
> <        my $rf = Bio::SeqFeature::Generic->new(-gff_string => 
> $feature->gff_string);
> <
> <        # now adjust the start and end positions in the new features on the 
> other strand
> <        # The feature is at position: length of the insertion-position. The 
> -1 is required, and I think I know why, but I am not sure I can explain it
> <        $rf->start($self->length-($rf->start-1));
> <        $rf->end($self->length-($rf->end-1));
> <        # now we have to correct the strand.
> <        if ($rf->strand == '-1') {$rf->strand(1)}
> <        elsif ($rf->strand == '1') {$rf->strand(-1)}
> <        $out->add_SeqFeature($rf);
> <     }
> <
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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
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