[Bioperl-l] Fwd: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/Microarray/Tools: use superclasses initialization and argument processing/ attribute setting as suggested in styleguide

Hilmar Lapp hlapp at gmx.net
Thu Dec 11 10:19:48 EST 2008


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
>>
>>
>
> _______________________________________________
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> Bioperl-l at lists.open-bio.org
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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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