[Bioperl-l] Bio::Restriction::IO and REBASE file

[Chris Fields]

Again, it's b/c 'withrefm' is a valid Restriction::IO module and  
'withref' is not.  Similar to the case issue you saw before with  
'bairoch.'  Making this more lenient would help but there are more  
serious issues with these modules that need to be addressed...

http://www.bioperl.org/wiki/Project_priority_list#Restriction_Enzymes

Chris

On May 26, 2006, at 3:55 PM, Jelena Obradovic wrote:

> Hi guys, I tried with the other formats, and it works fine with  
> "withrefm"
> format but not with "withref".
>
> Thanks a lot for your reponse.
>
> Cheers,
>
> Jelena
>
> On 5/26/06, Chris Fields <cjfields at uiuc.edu> wrote:
>>
>>
>>
>>> -----Original Message-----
>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>> bounces at lists.open-bio.org] On Behalf Of Jelena Obradovic
>>> Sent: Friday, May 26, 2006 11:47 AM
>>> To: Bioperl-l at lists.open-bio.org
>>> Subject: [Bioperl-l] Bio::Restriction::IO and REBASE file
>>>
>>> Hi there,
>>>
>>> I have tried loading enzyme list from a file REBASE bairoch.605  
>>> using
>>> Bio::Restriction::IO;
>>>
>>> 1. But for some reason the number of enzymes in the list is  
>>> always 532
>>> which is a default set of enzymes in enzyme collection.
>>>
>>> Is there any known issue with this module or a workaround?
>>>
>>> And here is the code I have been using:
>>>
>>> my $re_in=Bio::Restriction::IO->new(-file=>"bairoch_605.dat",-
>>> format=>"Bairoch")
>>> || die "can't load the file bairoch.605: $!";
>>> my $enzymes = $re_in->read;
>>> print "\nNo of enzymes: ", scalar $enzymes->each_enzyme, "\n";
>>
>> my $re_in=Bio::Restriction::IO->new(-file=>"bairoch_605.dat",-
>>                                    format=>"Bairoch");
>>
>> should be
>>
>> my $re_in=Bio::Restriction::IO->new(-file=>"bairoch_605.dat",-
>>                                    format=>"bairoch");
>>
>> Note the case change for the format; this is noted in the bug  
>> report you
>> submitted earlier.  Bio::Restriction::IO works similarly to  
>> Bio::SeqIO (
>> i.e.
>> requires a specific format, which I believe is case-sensitive).   
>> Judging
>> by
>> the modules in Bio/Restriction/IO directory, looks like the
>> Bio::Restriction::IO format should match one of the following  
>> formats:
>> bairoch, itype2, withrefm, and you can also build your own if  
>> needed using
>> the previous as examples and implementing Bio::Restriction::IO::base.
>>
>>> 2. The other problem is when trying to use format that is lower-case
>>> it throws an exception, but when "B" is capitalized it is ok.
>>> I assume it cannot load a file and does not initilize enzyme
>>> collection properly.
>>>
>>> Can't call method "each_enzyme" on an undefined value at
>>> .../cgi-bin/seq-load.pl line 51.
>>
>> My guess?  The reason it works with an uppercase ('Bairoch') is  
>> that it
>> can't find the module and uses the default set of enzymes as a  
>> fallback.
>> The exception that you reported when you use lowercase ('bairoch')  
>> is real
>> and I reported it as a bug (there are a few I found in that module).
>>
>> You might want to try using one of the other formats if you can  
>> get the
>> files in the right format from REBASE.  I'm looking into the bugs
>> specifically associated with Bio::Restriction::IO::bairoch.
>>
>>> Any thoughts?
>>>
>>>
>>> Thanks in advance,
>>>
>>>
>>> Jelena Obradovic
>>> jelenaob at gmail.com
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>
>
> -- 
> Jelena Obradovic
> Email: jobradovic at gmail.com
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign