[Bioperl-l] SimpleAlign changes

[Ewan Birney]

On Thu, 10 May 2001, Heikki Lehvaslaiho wrote:

> 
> Dear All,
> 
> Last week I decided to teach myself SimpleAlign. I found myself making
> corrections and changes into documentation as well as into code and
> writing dozens of tests. Before I commit anything, I'd like to list
> what I found.
> 
> 1. While Bio::AlignIO is declared to be a prefered way of reading in 
>    alignments, Bio::SimpleAlign contains a number of methods doing the 
>    same. Should't these be removed? Is all the funcionality of these 
>    methods in Bio::AlignIO? [not done]

for sure 

> 
> 2. The method names in SimpleAlign should follow bioperl conventions
>    (all lower case with words separated by undescores).
>    The old names could be left but documetation should point to new 
>    names. [done] Should depreciated names print a warning? [not done]
> 
>     	addSeq		->	add_seq
> 	eachSeq		->	each_seq
> 	eachSeqWithId	->	each_seq_with_id
>         length_aln	->	length
> 	removeSeq	->	remove_seq
> 

probably a good thing

> 
> 3. There seems to be two methods: maxname_length() and
> maxnse_lenght(), 
>    which are not used at all. There is a method
> maxdisplayname_lenght() 
>    which seems to have all the functionality needed. Can they be 
>    removed or pointed to maxdisplayname_length()[done]?
> 


I *think* so. Are you sure nothiing in the AlignIO use them?


> 4. Methods get_displayname() and set_displayname() should be merged 
>    into displayname() and a test should be added to prevent using 
>    nonexistant sequence names. (The method manipulates hashes directly 
>    and new keys are automatically created when used: autovivication!)
>    [done]
> 
>     Adding the test brough into light a problem: $seq->get_nse() is of 
>     form "name/start-end" and $aln->addSeq/add_seq was using form
>     "name-start-end". Changed '-' -> '/' in add_seq(). [done]
> 
> 5. Bio::LocatableSeq has this key method get_nse() which has a 
>    counterintuitive name. Couldn't we use name() while leaving the old 
>    name for backward compatibility. [done] 
> 

My view is that ->name is to ambiguous. nse stands for name-start-end
(just my view...)


>    Also, get_nse() accepts arguments 
>    for separator characters (/ and '). This seems to be a relic  
>    from pre-bioperl times.  Use of other characters needs be 
>    discouraged/ability removed? [not done]
> 

Nope - we need this for some other things

>    Method name/get_nse() needs internal tests to make sure that all
>    three values are set. [done]
> 
> 
> 6. Methods affecting all sequences in the alignment 
>    (set_displayname_count(), set_displayname_flat(), 
>    set_displayname_normal(), uppercase() ) need to return true (1) so 
>    that they can be tested. [done]
> 
> 7. Number of methods were calling depreciated PrimarySeqI methods. 
>    [fixed]
> 
> 8. Blast output parser Bio::Toold::BPbl2seq was leaving one space 
>    character to the end of the sequence id resulting a nonsatandard 
>    LocatableSeq name. [fixed]
> 


You are the man Heikki!  Really good work! Wow! 





> 
> 
> After my changes all the AlignIO test pass and SimpleAlign test count
> is up from 6 to 32. The only (non-IO) method that I did not test was
> purge().
> 
> 	-Heikki 
> 
> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
>      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> ___ _/_/_/_/_/________________________________________________________
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------