[Biopython-dev] problems pssm.search()

[Karen Sargsyan]

Hi all,

I'm going over the Motif part in the Biopython tutorial. Basically I'm 
trying to
repeat what is written in the "14.6.2  Searching for matches using the 
PSSM score " section:

or position, score in pssm.search(test_seq, threshold=3.0):
...     print("Position %d: score = %5.3f" % (position, score))

In my case test_seq is an amino acid sequence, pssm is successfully constructed over other amino acid sequences, or at
least I've got such an impression. You may notice that all the examples in this section of tutorial are
given for DNA only. So, I've discovered that proceeding with amino acids it not an easy task.
It is not mentioned anywhere that if you don't need search over reverse complement then there should be:

position, score in pssm.search(test_seq, threshold=3.0,*both=False*):

I've found last in the code, not in documentation. This is not worth mentioning in the developer's
mailing list, but later I've discovered in the code that pssm.search works with DNA only!!! (again nothing in docs about it).
I'm looking at the current source code in matrix.py on Github and following all those
error messages Biopython provides. So, the question is, why is that the case? Is this a deliberate decision based
on some arguments I don't see/know, or it is something that waits contributing the code? I feel it would
be helpful to mention those details in tutorial as well.
Thanks:)

With best regards,
Karen