[Biopython-dev] [Bug 3096] PPBuilder build_peptides bugs

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3096





------- Comment #7 from biopython-bugzilla at maubp.freeserve.co.uk  2010-09-09 13:58 EST -------
(In reply to comment #6)
> Hi Peter,
> 
> I tested out the code (on the script directly, not using git) and it works
> fine.

Excellent - thank you.

> I only have minor concerns that the additional input variable
> "standard_aa_only" for _accept() method in class _PPBuilder might break
> other codes that assumes it still has two instead of three input variables. 

True, but I think that is a low risk and it is intended as a private API.
It could be made an optional argument I suppose.

> Also within the same script there are three different naming and default value
> for the same flag (standard amino acid):
> 
> 1. named "standard" with default False in is_aa() method
> 2. named "aa_only" with default 1 in build_peptides() method of class
> _PPBuilder
> 3. named "standard_aa_only" with no default value in _accept() method of class
> _PPBuilder
> 
> Which is again minor. 

We can change the new argument ("standard_aa_only") added to _accept() without
breaking backwards compatibility. I was trying to make it explicit - would you
prefer "standard" instead? We both agreed that "aa_only" is very misleading.

Peter


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.