[Bioperl-l] Bio::SeqIO::staden::read make test error

Roy Chaudhuri roy.chaudhuri at gmail.com
Tue Apr 14 10:54:21 EDT 2009

Hi Mike.

I did get that problem solved in the end, thanks to lots of help from 
Aaron Mackey. Looking at the bioperl-l archives it seems like we stopped 
cc-ing the mailing list at some point. The last archived message in the 
thread (http://bioperl.org/pipermail/bioperl-l/2005-May/018925.html) had 
the correct solution - the code change was incorporated into the 
bioperl-ext CVS, and is in the latest version that you can get from SVN 
(see http://www.bioperl.org/wiki/Ext_package). If that doesn't solve the 
problem you must be experiencing a different issue.

You should also bear in mind the message Chris Fields sent to the list a 
few days ago, and have a look at using BioLib instead:

> Just to note, we're not actively supporting much of the bioperl-ext  
> code, in favor of the BioLib initiative:
> http://biolib.open-bio.org/wiki/Main_Page
> If you do use bioperl-ext I suggest only using the latest code from  
> svn (and that in combination with bioperl-live).
> chris

Hope this helps.

Michael Stubbington wrote:
> Dear Dr. Chaudhuri,
> I am currently trying to write a bioperl script that parses .abi 
> sequence files. I am having exactly the same problem as you did when
> you posted this enquiry to the bioperl mailing list 
> http://bioperl.org/pipermail/bioperl-l/2005-May/018898.html. I was 
> wondering if you ever solved the problem and, if so, can you remember
>  what you did? I’d be very grateful for any help you can provide. I
> can’t find this problem mentioned anywhere else online.
> Thank you for your time.
> Mike

Dr. Roy Chaudhuri
Department of Veterinary Medicine
University of Cambridge, U.K.

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