[Bioperl-l] get_sequence error retrieving protein sequences from GenBank

[Warren Alden Kibbe]

This is an odd problem that I have seen in the get_sequence call for 
genbank accession numbers that are for protein rather than DNA 
entries. One of my colleagues, Julie Zhu, has reported the bug at 
http://bugzilla.bioperl.org with bug# 1545 a week or two ago and 
still waiting for response.

The detailed bug information is as follows:

The following two protein accession numbers are valid by searching 
through the ncbi protein database. However, bioperl 1.2.3 
get_sequence complains that the accession number  does not exist. The 
bioperl 1.2.3 get_sequence for the corresponding DNA accession 
numbers works fine. Please note that one is for genbank and the other 
is for embl (Both swissprot and refseq entries work fine).

$seq_object = get_sequence('genbank', "AAQ10714");#protein accession 
number does not work
$seq_object = get_sequence('genbank', "AF536179"); #DNA accession number works

$seq_object = get_sequence('embl',"CAD32973"); #protein accession 
number does not work
$seq_object = get_sequence('embl',"AJ489231"); #DNA accession number works

Does anyone else see this behavior? We see on under Perl 5.61 and 
Perl 5.8 running bioperl 1.2.3 on both Mac OS X and Windows 2000. 
Thank you very much for your time and help in advance.

Warren