[Bioperl-l] problem unigene parsing

[Hilmar Lapp]

On Wednesday, March 5, 2003, at 06:31  PM, Siddhartha Basu wrote:

> 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.

The reason is C.elegans wasn't in the species abbreviation map table. I 
updated the table to match the present NCBI repository and migrated the 
fix to the branch too.

> And the lines contain the species name in Unigene files is the PROTSIM 
> segment.

I may be mistaken, but I don't think this is a given for every entry.

> 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.

If you inspect the message you see that it does get the array in the 
right order.

	-hilmar

>
>
> 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.
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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