[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

Chris Fields cjfields at illinois.edu
Wed Dec 10 13:59:41 EST 2008


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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