[Bioperl-l] problem with batch access to GenBank

Anne-Marie Ternes amternes at pt.lu
Tue Jun 3 20:11:26 EDT 2003


I've got a problem for submitting a batch of gene accession numbers to 

I simply use the Bio::DB::GenBank package for creating a new GenBank 
instance, and then use the "get_Stream_by_acc" method, passing it an 
array of accession numbers as parameter.
Unfortunately, I don't get any results from this query. It seems to run 
OK, as I get no connection error messages, it just ignores my subsequent 
"while" loop looking for the next sequence in the result set.

Although I'm a PERL newbie, I'm not a network dummy, so I'm totally sure 
I'm not behind a proxy, nor behind a firewall. I have unset any 
environment variables related to proxies.
I'm also sure that the array effectively contains accession numbers in 
correct formats.

Another bit of code, that resembles the problematic one for one single 
difference: it uses "get_Seq_by_acc" with a single accession number as 
parameter, runs perfectly:
information regarding enzyme numbers are correctly retrieved, and later 
passed to a KEGG query.

So I wonder if there might be some obscure difference in implementation 
between "get_Seq_by_acc" and "get_Stream_by_acc".

By the way, I have also checked using "netstat" that connections to NCBI 
get properly established, which is the case.

If anyone has an idea what might be going on, I can't say how glad I'd 
be! I'm in fact a bioinformatics MSc student, and ironically, my code 
runs perfectly on my pal's computers, but not on mine ;-)

Thanks a lot in advance,

Anne-Marie Ternes
amternes at pt dot lu

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