[Bioperl-l] BioC and BioPerl Re: Fwd: [Bioperl-guts-l] [15134] yadayadayada

Chris Fields cjfields at illinois.edu
Thu Dec 11 16:27:04 UTC 2008 

Yes.  This is the way I intended to go (swig-based, so can apply to  
other Bio*).  The initial release already has some links to the  
affymetrix library (http://biolib.open-bio.org/wiki/ 
BioLib_Affymetrix), but that's independent of R.

chris

On Dec 11, 2008, at 9:19 AM, Hilmar Lapp wrote:

> You guys do know about the BioLib project?
>
> http://biolib.open-bio.org/wiki/Main_Page
>
> Bridging R and BioC to the Bio* projects is one of the core goals if  
> I remember correctly.
>
> 	-hilmar
>
> On Dec 11, 2008, at 9:55 AM, Chris Fields wrote:
>
>> Just need a decently-supported perl-R package to help along those  
>> lines.  RSPerl might work, but I find it too problematic to work  
>> with on my Mac OS and it isn't well-supported (doesn't find my  
>> local perl installation so mixes libraries and, well, crashes  
>> during compilation).
>>
>> The best bridging would generically bring R into perl (and BioC  
>> into BioPerl).  Statistics::R is a pure perl method but it appears  
>> pretty messy.  I may toy around with an XS-based solution myself  
>> after 1.6 is out.
>>
>> chris
>>
>> On Dec 11, 2008, at 4:12 AM, Marian thieme wrote:
>>
>>> I also had the impression that "it" was discouraged to use bioperl  
>>> for microarray processing.
>>> As I know from my colleagues and also I did to good extemt) people  
>>> use R (especially Bioconductor) for most of the issues concerning  
>>> microarrays. (there are so many supoorted microarray designs,  
>>> preprocessing and normalization tools, and complete packages to  
>>> perform differential expression analysis). At least for the  
>>> expression chips but also for genotyping/SNP chips I think R/BioC  
>>> is method of choice. Probably for the resequencing chips they are  
>>> not that well supported, because its only a minority that uses  
>>> this kind of chips. Therefore I think ReseqChip has its right to  
>>> exist, even though it would reach more people if it would a R/BioC  
>>> package. (Moreover I believe that this kind of chips wont have  
>>> broader interest, because second generation sequencing methods  
>>> will probably be more appropriate in the next few years)
>>> So to cut a long story short, I find Chris' idea of bridging  
>>> bioperl to BioC (or vice versa) very good: Dont compete against R/ 
>>> BioC, but make it easier to use both together.
>>>
>>> marian
>>>
>>>
>>> Marian Thieme
>>> Institute of Functional Genomics
>>> University Regensburg
>>> Josef Engert Str. 9
>>> 93053
>>> Regensburg
>>> Germany
>>> P: 0049 (0)941 943 1584
>>> F: 0049 (0)941 943 5020
>>> E:  marian.thieme at klinik.uni-regensburg.de
>>> W: http://www-cgi.uni-regensburg.de/Klinik/FunktionelleGenomik
>>>
>>>
>>>>>> Chris Fields <cjfields at illinois.edu> 12/10/2008 7:59 PM >>>
>>> Sounds like a good idea, with one caveat: Allen had pretty much  
>>> given
>>> up on bioperl-microarray last I heard (last significant commits were
>>> ~6 yrs ago).  It would be nice to revive with this theme in mind,
>>> though maybe bioperl-expression would be better (could focus on  
>>> other
>>> expression-related issues along with microarray data).  Marian, what
>>> do you think?
>>>
>>> chris
>>>
>>> P.S. An aside: I'm planning on running lots of Illumina data myself
>>> and have been thinking about making a BioC-BioPerl bridge, then  
>>> seeing
>>> how it fits into a bioperl-microarray.  Just need a working perl-R
>>> interface (NOT RSPerl).
>>>
>>> On Dec 10, 2008, at 12:42 PM, Jason Stajich wrote:
>>>
>>>> Since we've started discussing the idea of starting to move things
>>>> out into smaller packages, does it make sense to move this
>>>> Bio::Microarray into its own package before it gets bigger? What
>>>> about the old bioperl-microarray stuff from Allen Day?
>>>>
>>>> I also know that as we haven't branched for 1.6 Chris we'll have to
>>>> make some decisions about new code going in before then?
>>>>
>>>> Not trying to stifle any of the development with extra work but
>>>> trying to see if we should start to make some logical slices of
>>>> packages?
>>>>
>>>> -jason
>>>>
>>>> Begin forwarded message:
>>>>
>>>>> From: Marian Thieme <thm09830 at dev.open-bio.org>
>>>>> Date: December 10, 2008 6:10:21 AM PST
>>>>> To: bioperl-guts-l at bioperl.org
>>>>> Subject: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/ 
>>>>> Microarray/
>>>>> Tools: use superclasses initialization and argument processing/
>>>>> attribute setting as suggested in styleguide
>>>>>
>>>>> Revision: 15134
>>>>> Author:   thm09830
>>>>> Date:     2008-12-10 09:10:21 -0500 (Wed, 10 Dec 2008)
>>>>>
>>>>> Log Message:
>>>>> -----------
>>>>> use superclasses initialization and argument processing/attribute
>>>>> setting as suggested in styleguide
>>>>>
>>>>> Modified Paths:
>>>>> --------------
>>>>> bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm
>>>>> bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm
>>>>>
>>>>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ 
>>>>> MitoChipV2Parser.pm
>>>>> = 
>>>>> ==================================================================
>>>>> --- bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm	
>>>>> 2008-12-10 12:51:47 UTC (rev 15133)
>>>>> +++ bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm	
>>>>> 2008-12-10 14:10:21 UTC (rev 15134)
>>>>> @@ -78,12 +78,13 @@
>>>>>
>>>>> sub new {
>>>>>
>>>>> -  my ($class, $file_name) = @_;
>>>>> -  my $self = $class->SUPER::new();
>>>>> +  my ($class, @args) = @_;
>>>>> +  my $self = $class->SUPER::new(@args);
>>>>> +  my ($file_name)=$self->_rearrange([qw(AFFY_DESIGN_FILENAME)],
>>>>> @args);
>>>>> +
>>>>> $self->{_frags_hash}=undef;
>>>>> $self->{_oligos2calc_hash}=undef;
>>>>> $self->throw("Must provide filename as first argument !") unless
>>>>> $file_name;
>>>>> -
>>>>>
>>>>> my %max_ins_hash=();
>>>>> $self->{_frags_hash}=$self-
>>>>>> _parse_Affy_mtDNA_design_annotation_file($file_name);
>>>>>
>>>>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm
>>>>> = 
>>>>> ==================================================================
>>>>> --- bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm	 
>>>>> 2008-12-10
>>>>> 12:51:47 UTC (rev 15133)
>>>>> +++ bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm	 
>>>>> 2008-12-10
>>>>> 14:10:21 UTC (rev 15134)
>>>>> @@ -194,8 +194,11 @@
>>>>>
>>>>> sub new {
>>>>>
>>>>> -  my ($class, $design_file_name, $format, $refseq_max_ins_hash,
>>>>> $refseq) = @_;
>>>>> -  my $self = $class->SUPER::new();
>>>>> +  #my ($class, $design_file_name, $format, $refseq_max_ins_hash,
>>>>> $refseq) = @_;
>>>>> +  my ($class, @args) = @_;
>>>>> +  my $self = $class->SUPER::new(@args);
>>>>> +  my ($design_file_name, $format, $refseq_max_ins_hash, $refseq)=
>>>>> $self->_rearrange([qw(AFFY_DESIGN_FILENAME FORMAT_OF_DESIGN_FILE
>>>>> MAX_INSERTION_HASH_REFERENCE REFERENCE_SEQUENCE)], @args);
>>>>> +
>>>>> $self->{_frags_hash}=undef;
>>>>> $self->{_max_ins_hash}=undef;
>>>>> $self->{_refseq}=undef;
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-guts-l mailing list
>>>>> Bioperl-guts-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l
>>>>
>>>> Jason Stajich
>>>> jason at bioperl.org
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>

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