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

Chris Fields cjfields at illinois.edu
Thu Dec 11 16:32:40 UTC 2008


Oops, my bad.  This does involve R's affyio.  Will have to investigate  
after 1.6.

http://github.com/pjotrp/biolib/tree/master/src/clibs/affyio-1.8/README_BIOLIB

chris

On Dec 11, 2008, at 10:27 AM, Chris Fields wrote:

> 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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