[Bioperl-l] sanity check my understanding of bioperl's location terminology?
hartzell at alerce.com
Tue Oct 21 23:48:09 EDT 2008
Heikki Lehvaslaiho writes:
> You've got it all right expect the last bit.
> Bio::LocatableSeq::column_from_residue_number() is a special case because it's
> input is in original sequence coordinates, of which the LocatableSeq in
> question is part of.
> Look at the tests. I just added a few on column_from_residue_number() that
> show that if you take a revcom() on a LocatebleSeq the outcome of this method
> remains the same! The reason is that within a same alignment, a revcomed
> sequence is not a the same one any more. You can not put it back into the same
> The following demonstrates it by taking two sequences that happen to have
> almost identical in the wrong strand (I hope I did not mess this up by doing
> it by hand):
> seq1 ttaccta
> seq2 atgctat
I think that it should be
so that it matches the alignment in the example below.
> seq1 --atg---gtaa- -1
> seq2 --atg---ctat- 1
> is $seq1->column_from_residue_number(5),5;
> is $seq1->column_from_residue_number(4),9;
> is $seq2->column_from_residue_number(5),10;
> is $seq2->column_from_residue_number(4),9;
> Maybe Ewan can be dragged from his bioperl retirement to point us to an old
> document somewhere that explains all the logic behind the way strand is used
> in bioperl?
It's great to have it all broken out, written down, and commited to
It even makes sense, in that way that only things involving strand
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