[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

[Marian thieme]

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;
>>
>>
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>
> Jason Stajich
> jason at bioperl.org
>
>
>
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