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

[Chris Fields]

Heikki,

I mainly just changed a few things so no one would get the wrong  
ideas from POD (that they write format as well) and added a few  
things to the TO DO.  I also added a warning to  
Bio::Restriction::IO::bairoch for the multisite/multicut issue.   
Besides that I haven't done much to them.  I also added a bit to the  
Project Priority List in case someone wants to take it up.  I may  
tinker with it but it's not really high on my priority list.  I've  
been pretty busy getting the ListSummaries back up to speed (very  
busy mail lists since the last one) and am writing/testing a new  
interface to NCBI EUtilities which I may donate at some in the next  
few months or so.

Chris


On May 31, 2006, at 5:44 AM, Heikki Lehvaslaiho wrote:

>
> 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
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/
>      _/  _/  _/  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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign