[Bioperl-l] RE: Bio::Tools::EPCR.pm patch request

[Cook, Malcolm]

Jason,

Wow!  You the man!  That was fast.  I see it in the cvs change log
already...

But...

Would you mind reinstating the tiny additional change I made to only
produce the note tag value if $rest is present.  I'm using it in an
applicatoin where there are no addition columns in my e-PCR input file,
and am getting an empty note attribute on each GFF line....

There may be a better way of coding it than:
	
 $markerfeature->add_tag_value('Note',$rest) if $rest;

Thanks,

Malcolm

>-----Original Message-----
>From: Jason Stajich [mailto:jason at cgt.duhs.duke.edu] 
>Sent: Monday, March 15, 2004 3:29 PM
>To: Cook, Malcolm
>Cc: Bioperl
>Subject: Re: Bio::Tools::EPCR.pm patch request
>
>
>done!
>
>I added the ability to the update the primary,source,groupclass fields
>using get/set methods as well. I also capitalized the 'Note' 
>field to be
>in line with the way GFF3 looks.
>
>-j
>On Mon, 15 Mar 2004, Cook, Malcolm wrote:
>
>> Jason,
>>
>> I'd like it if you would accept and apply the following diff 
>to the very
>> useful Bio::Tools::EPCR module.   I hope you agree that it 
>provides more
>> flexibility in defining the structure of the features that 
>are produced
>> (and, ultimately for me, the format of the GFF which gets 
>written before
>> being loaded into Bio::DB::GFF database).
>>
>> I have made the behaviour completely backwards compatible.
>>
>> Sincerely,
>>
>> Malcolm Cook - mec at stowers-institute.org - 816-926-4449
>> Database Applications Manager - Bioinformatics
>> Stowers Institute for Medical Research - Kansas City, MO  USA
>>
>> Index: EPCR.pm
>> ===================================================================
>> RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/EPCR.pm,v
>> retrieving revision 1.8
>> diff -c -r1.8 EPCR.pm
>> *** EPCR.pm	2002/12/01 00:05:21	1.8
>> --- EPCR.pm	2004/03/15 20:27:04
>> ***************
>> *** 92,110 ****
>>   =head2 new
>>
>>    Title   : new
>> !  Usage   : my $epcr = new Bio::Tools::EPCR(-file => $file);
>> !  Function: Initializes a new EPCR parser
>>    Returns : Bio::Tools::EPCR
>>    Args    : -fh   => filehandle
>>              OR
>>              -file => filename
>>
>>   =cut
>>
>>   sub new {
>>     my($class, at args) = @_;
>>
>>     my $self = $class->SUPER::new(@args);
>>     $self->_initialize_io(@args);
>>
>>     return $self;
>> --- 92,120 ----
>>   =head2 new
>>
>>    Title   : new
>> !  Usage   : my $epcr = new Bio::Tools::EPCR(-file => $file, 
>-primary =>
>> $fprimary, -source => $fsource, -groupclass => $fgroupclass);
>> !  Function: Initializes a new EPCR parser.
>>    Returns : Bio::Tools::EPCR
>>    Args    : -fh   => filehandle
>>              OR
>>              -file => filename
>>
>> +            -primary => a string to be used as the common value for
>> each features '-primary' tag.  Defaults to 'sts'.  (This in 
>turn maps to
>> the GFF 'type' tag (aka 'method')).
>> +
>> +            -source => a string to be used as the common 
>value for each
>> features '-source' tag.  Defaults to 'e-PCR'. (This in turn 
>maps to the
>> GFF 'source' tag)
>> +
>> +            -groupclass => a string to be used as the name 
>of the tag
>> which will hold the sts marker namefirst attribute.  
>Defaults to 'name'.
>> +
>>   =cut
>>
>>   sub new {
>>     my($class, at args) = @_;
>>
>>     my $self = $class->SUPER::new(@args);
>> +   my ($primary, $source, $groupclass) = 
>$self->_rearrange([qw(PRIMARY
>> SOURCE GROUPCLASS)], at args);
>> +   $self->{'_primary'} = $primary || 'sts';
>> +   $self->{'_source'} =  $source || 'e-PCR';
>> +   $self->{'_groupclass'} =  $groupclass || 'name';
>>     $self->_initialize_io(@args);
>>
>>     return $self;
>> ***************
>> *** 139,152 ****
>>       my $markerfeature = new Bio::SeqFeature::Generic ( 
>'-start'   =>
>> $start,
>>   						       '-end'     =>
>> $end,
>>   						       '-strand'  =>
>> $strand,
>> ! 						       '-source'  =>
>> 'e-PCR',
>> ! 						       '-primary' =>
>> 'sts',
>>   						       '-seq_id'  =>
>> $seqname,
>>   						       '-tag'     => {
>> ! 							   'name'=>
>> $mkrname,
>> ! 							   'note'=>
>> $rest,
>>   						       });
>>       return $markerfeature;
>>   }
>>
>>   1;
>> --- 149,163 ----
>>       my $markerfeature = new Bio::SeqFeature::Generic ( 
>'-start'   =>
>> $start,
>>   						       '-end'     =>
>> $end,
>>   						       '-strand'  =>
>> $strand,
>> ! 						       '-source'  =>
>> $self->{'_source'},
>> ! 						       '-primary' =>
>> $self->{'_primary'},
>>   						       '-seq_id'  =>
>> $seqname,
>>   						       '-tag'     => {
>> !
>> $self->{'_groupclass'}=> $mkrname,
>>   						       });
>> +     $markerfeature->add_tag_value('note',$rest) if $rest;
>>       return $markerfeature;
>> +
>>   }
>>
>>   1;
>>
>
>--
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu
>