[Bioperl-l] Bio::Restriction::IO issues

[Heikki Lehvaslaiho]

Chris,

Thanks for stepping in. I feel partly responsible here because I originally 
changed some of Rob's code but have not followed up since.

There have not been active development on these modules so do not worry about 
stepping on anyone's toes.

   -Heikki

On Tuesday 30 May 2006 16:50, Chris Fields wrote:
> Jason, Brian, et al,
>
> I found several major issues with Bio::Restriction::IO (this popped up
> while bug squashing).  In particular, the POD is pretty misleading.  It
> states (directly from perldoc):
>
> SYNOPSIS
>         use Bio::Restriction::IO;
>
>         $in  = Bio::Restriction::IO->new(-file => "inputfilename" ,
>                                          -format => 'withrefm');
>         $out = Bio::Restriction::IO->new(-file => ">outputfilename" ,
>                                          -format => 'bairoch');
>         my $res = $in->read; # a Bio::Restriction::EnzymeCollection
>         $out->write($res);
>
>       # or
>
>       #    use Bio::Restriction::IO;
>       #
>       #    #input file format can be read from the file extension (dat|xml)
>       #    $in  = Bio::Restriction::IO->newFh(-file => "inputfilename");
>       #    $out = Bio::Restriction::IO->newFh('-format' => 'xml');
>       #
>       #    # World's shortest flat<->xml format converter:
>       #    print $out $_ while <$in>;
>
> So, I have found several problems with these modules.  I really hate to
> criticize code here, as my own is pretty hacky, but I think these are
> things to seriously mull over:
>
> 1)	Note that, though some of the lines above are commented they are
> still there in POD and thus present in perldoc/pod2html etc.  So, judging
> from the above, it suggests using the script above should read in from one
> format and write out to another (like SeqIO).  However, NONE of the current
> write() methods are implemented for any of the IO modules (withref, base,
> itype2, bairoch), so this does not happen as expected.  You get the nasty
> thrown 'method not implemented error' instead when writing.
> 2)	The commented statements in POD above also suggest that REBASE XML
> format is supported when there is no XML module.
> 3)	The Bio::Restriction::IO::bairoch module had multiple bugs which
> made it unusable until I added a few small changes; it still can't handle
> multisite/multicut enzymes properly, so in essence it is useless until that
> is addressed.
> 4)	Bio::Restriction::IO inherits from Bio::SeqIO, though I'm not sure
> why.  Shouldn't it just inherit from Bio::Root::Root/Bio::Root::IO and make
> up it's own methods?
>
> I'm working on at least getting the 'bairoch' input format up and running
> (so at least it gets the enzymes into a
> Bio::Restriction::Enzyme::Collection).  From this point I'm not sure where
> to proceed.  The POD obviously needs to be corrected to reflect that
> writing formats is not implemented (and the bit about XML should be taken
> out completely); that's the easy part which I am working on and plan
> committing today.  However, these modules don't seem to be used too
> frequently so I'm not sure whether it's worth spending too much time
> getting these up to speed at the moment (adding write methods, switching to
> Bio::Root::Root, etc); I have other priorities at the moment (including a
> way overdue ListSummary). I'm also not sure who else is (using|working) on
> these so I don't want to (make too many changes|step on someone else's
> toes), but these are, IMHO, pretty serious problems.
>
> Any thoughts?
>
> Chris
>
>
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
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-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of the Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
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