[Bioperl-l] Bio::UnivAln mourned

Dave NO SPAM Ardell myfirstname-DOT-mylastname at icm.uu.se
Sat Jan 31 08:17:04 EST 2004


After some egging on by somebody else I am taking public a problem or  
I am having in latest releases of bioperl and some suggested solutions.

I miss Bio::UnivAln! Seems to me it has functionality missing
in Bio::SimpleAlign. For instance, functions that operate on the  
content like Bio::UnivAln::var_sites, Bio::UnivAln::no_allgap_sites, or
Bio::UnivAln::map_c. I also like the added flexibility
in its constructor, slicing functions, and in manipulating sequences
by name.

This is not to say I could do without Bio::SimpleAlign, for instance,  
column_from_residue_number functionality is not represented in
UnivAln.  I have quite a few scripts that use both modules together.

I guess I never felt the removal of Bio::UnivAln before because it
was still sitting there from old installs when I'd upgrade Bioperl.

But I just migrated from linux to OS X, and my latest install (bioperl  
was virgin to my new machine.

After my scripts carped I placed UnivAln.pm from an old bioperl dist (I  
used 0.7.0)
into my bioperl-1.x build tree (install-dist/Bio) and added it's name  
before running (or re-running) perl Makefile.PL.

Now it works without apparent conflicts in my set-up, YMMV.

I understand that maybe the demise of the module is due to its lack of  
a maintainer keeping its
guts up-to-date with bioperl root structure. I would perhaps be willing  
to help here.
Would there be objections to its revival? Or are there plans to expand  
existing modules?


David Ardell, Asst. Professor.  			tel   : 46 (0) 18 471 6694
Linnaeus Centre for Bioinformatics		fax  : 46 (0) 18 471 6698
Uppsala University Biomedical Center      http://www.lcb.uu.se/~dave
Husargatan 3, Box 598,				
SE 751 24 Uppsala SWEDEN.

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