[Bioperl-l] problem unigene parsing

[Siddhartha Basu]

Hi andrew,
Yes you got the problem it seems. Well i really can't say anything in 
depth about the code but can point out the fact it's not really 
happening with the C.elegans unigene build file.And the lines contain 
the species name in Unigene files is the PROTSIM segment.
So there also seems to be problem with the bleeding edge version of 
bioperl. I haven't tried the stable 1.2 version for this parsing, only 
used it from the bioperl-live cvs. And moreover, by seeing the pod of 
Bio::Species i think  somehow the species->classification method call 
getting the name "Home sapiens" from the unigene object instead of 
"sapiens Homo" which it expect and might be generating the error. Just a 
guess though.


siddhartha



Andrew Macgregor wrote:
> Hi Siddhartha,
> 
> Yes I can reproduce this problem. When a Unigene object is created it 
> uses Species.pm that has this code segment that seems to print the 
> message you are getting (I think). Can anyone else help me out as to why 
> this is happening?
> 
> 
>   if( defined $classification &&
>       (ref($classification) eq "ARRAY") ) {
>       print "classification was @$classification\n";
>       $self->classification(@$classification);
>   }
> 
> -- Andrew.
> 
> 
>