[Bioperl-l] strange problem

Chris Fields cjfields at uiuc.edu
Thu Mar 29 12:26:34 EDT 2007


The issue with Build.PL may be that it is trying to update  
Scalar::Util to the latest (1.19) or install it if it isn't present  
but doesn't have the correct permissions.  I myself have run into  
this problem; you must install the latest Scalar::Utils directly via  
CPAN with the correct permissions ('sudo cpan' in my case).  I'm  
guessing that using something like 'sudo perl Build.PL' should work  
as well.

I'm adding Sendu to this so he can answer.  Sendu, I know it's now  
required for Bio::Species/Bio::Taxon stuff to weaken refs but was  
there any reason why Scalar::Util needs to be v1.19?  I can't recall  
anything about it in past discussions...

chris

On Mar 29, 2007, at 10:59 AM, Patricia Rodriguez Tome wrote:

> Hello Chris
>
> I took the bioperl from cvs (from the web site, did a tarball) but  
> now I am at lost to install it.
> Now that it does not use simple perl Makefile.PL, it wants to  
> install plenty of things with CPAN, and even complaints that my  
> CPAN has serious problems (I can install other things)
> So I am afraid that the test with the new cvs version will have to  
> wait another week until I come back and can solve all these problems
>
> In the meantime I am opening another bug with another very strange  
> case (I seem to be collecting them lately:)
> cheers
>
>
>
> Chris Fields wrote:
>> This is a bug.  Could you add this to bugzilla with a  
>> representative  report and script?  It should be easy to fix as  
>> it's likely just a  regex problem.
>>
>> http://www.bioperl.org/wiki/Bugs
>> http://bugzilla.open-bio.org/
>>
>> chris
>>
>> On Mar 22, 2007, at 9:11 AM, Patricia Rodriguez Tome wrote:
>>
>>
>>> Hi
>>>
>>> I have found a parsing problem in  SearchIO
>>> I have this result:
>>>
>>>                                                                    
>>> Score    E
>>> Sequences producing significant alignments:                        
>>> (bits) Value
>>>
>>> UniRef50_Q9X0H5 Cluster: Histidyl-tRNA synthetase; n=4;   
>>> Thermoto...    23     650
>>>
>>>
>>>
>>> I do a very simple parsing with SearchIO
>>> my $in = new Bio::SearchIO(-format => 'blast',
>>>                            -file => $ARGV[0]);
>>>
>>> while (my $hit = $result->next_hit()) {
>>>   print "name\t", $hit->name, "\n";
>>>   print "length\t", $hit->length, "\n";
>>>   print "accession\t", $hit->accession, "\n";
>>>   print "description\t", $hit->description, "\n";
>>>   print "raw_score\t", $hit->raw_score, "\n";
>>>   print "significance\t", $hit->significance, "\n";
>>>   print "bits\t", $hit->bits, "\n";
>>>
>>> And the result is:
>>> name    UniRef50_Q9X0H5
>>> length  420
>>> accession       UniRef50_Q9X0H5
>>> description     Cluster: Histidyl-tRNA synthetase; n=4;
>>> Thermotogaceae|Rep: Histidyl-tRNA synthetase - Thermotoga maritima
>>> raw_score       ...
>>> significance    23
>>> bits    22.7
>>>
>>> As you see the three dots at the end of description get into the raw
>>> score instead, then the evalue gets the raw score
>>> I am using bioperl1.5.1 and tried even with 1.5.2 but get the  
>>> same  result
>>> Where can I change it ?
>>>
>>> Grazie
>>>
>>> Patricia
>>>
>>> -- 
>>> Dr. Patricia Rodriguez-Tomé, PhD
>>> CRS4 - Bioinformatics
>>> Loc. Pixina Manna Edificio 3
>>> Pula 09010 (CA), Italy
>>> http://www.bioinformatica.crs4.org
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
> -- 
> Dr. Patricia Rodriguez-Tomé, PhD
> CRS4 - Bioinformatics
> Loc. Pixina Manna Edificio 3 Pula 09010 (CA), Italy
> http://www.bioinformatica.crs4.org
>
>

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






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