[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

Thu Dec 11 14:55:36 UTC 2008

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
>
>