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

[Jason Stajich]

oops - my fault - I missed that accidently - had trouble applying the
patch so was doing it by hand.  will do.

-jason


On Mon, 15 Mar 2004, Cook, Malcolm wrote:

> 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
> >
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu