Steve's notes on Seq.pm

[Steven E. Brenner]

Thanks for writing up all the notes!


> Perhaps we can kick
> these notes around and come up with a "MUST DO NOW" list of essentials that
> need to be fixed prior to the next version?

The essentials are things which either:

 1) Are seriously broken (very very few)
 2) Alter the interface (some)


> Personally, I feel that moving all ReadSeq stuff into a ReadSeq.pm would be
> worth the effort at this point.

Until we figure out how parsing and IO is going to be done, I would say
the interface isn't fixed.  So, yes, this is very important.


> o Perhaps we need another option for sequence type
>   that deals with alphabet stringency levels
>   1 Strict    1 Gap
>   2 Ambig     2 No-Gap   (2,1) Set as default?
A third option would be "on" or "off"



> 3. Settle the "_nofile" or "undef" question
>    in the constructor method
Georg agreed to _undef for Bio::UnivAln, so I think that makes sense here.


> 6. _file_read() is innefficient, just slurp file in with
>    a giant READ
Inefficiency like this is ok for now, I think.  But it should be fixed
very soon.


> 7. Resolve this conflict: names() currently will ADD the values
>    of a passed in hash referance to the existing %names hash.
>    However, the POD docs state that the method SETS (overwrites)
>    the hash values. Which should it do?
Let's make it 'set'


> **13. DNA_to_RNA() should return a Bio::Seq object, not a
>       string or array
> 
> **14. translate() should return a Bio::Seq object, not a
>       string or array

** Yes. :)  (Why the **?)


> 17. rename seq_length() to seq_len()


> 18. rename ary() and str() to seq_ary() and seq_str()
Actually, I've changed my mind about this, and think it might be better to
leave it as-is.  I can give my rationale if people care.