[Bioperl-l] sanity check my understanding of bioperl's location terminology?

George Hartzell hartzell at alerce.com
Tue Oct 21 23:48:09 EDT 2008


Heikki Lehvaslaiho writes:
 > George,
 > 
 > 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 
 > alignment.
 > 
 > 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

 seq1  ttaccat

so that it matches the alignment in the example below.

 >       1234567890123
 > 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?
 > 
 >    -Heikki
 > [...]

Thanks!

It's great to have it all broken out, written down, and commited to
the tree.

It even makes sense, in that way that only things involving strand
can.

g.



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