[Bioperl-l] locuslink.pm questions (for Keith Ching/Hilmar ?)

[Andrew Macgregor]

Hi,

I am using the locuslink.pm with SeqIO to read the LL_tmpl file and was 
just wondering about data that are left out.

1. Looking at locusid 1 and 2. The first record begins:

 >>1
LOCUSID: 1
LOCUS_CONFIRMED: yes
LOCUS_TYPE: gene with protein product, function known or inferred
ORGANISM: Homo sapiens
STATUS: REVIEWED
NM: NM_130786|21071029|na
NP: NP_570602|21071030
CDD: Immunoglobulin C-2 Type|smart00408|104|na|4.466900e+01
PRODUCT: alpha 1B-glycoprotein
ASSEMBLY: AF414429,AK055885,AK056201

The second record begins:

 >>2
LOCUSID: 2
LOCUS_CONFIRMED: yes
LOCUS_TYPE: gene with protein product, function known or inferred
ORGANISM: Homo sapiens
STATUS: REVIEWED
NM: NM_000014|6226959|na
NP: NP_000005|4557225
CDD: Ependymins|EPEND|86|na|3.773540e+01
CDD: Alpha-2-macroglobulin family|pfam00207|2501|na|9.679920e+02
CDD: Alpha-2-macroglobulin family N-terminal 
region|pfam01835|1889|na|7.322500e+02
PRODUCT: alpha 2 macroglobulin precursor
ASSEMBLY: M11313

In the first record the CDD line doesn't appear to be stored at all. In 
the second record the first CDD line is stored ie the one beginning 
with "Ependymins" but the other two are not. I was wondering about the 
logic behind this.


2. Also wondering about things like LOCUS_CONFIRMED and STATUS and why 
these are left out.

3. Lastly, and this is very nit-picking ;) but thought you might want 
it pointed out for consistency...

In Bio::Annotation::OntologyTerm the as_text() method does something 
different than it says it will, and different to other as_text() 
methods. ie it doesn't print "Value: "

=head2 as_text

  Title   : as_text
  Usage   : my $text = $obj->as_text
  Function: return the string "Name: $v" where $v is the name of the term
  Returns : string
  Args    : none


=cut

sub as_text{
    my ($self) = @_;

    return $self->tagname()."|".$self->name()."|".$self->identifier();
}

-- Andrew.