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

Joel Martin j_martin at lbl.gov
Wed Apr 15 02:50:37 EDT 2009

   Do you know where it says io_lib will stop supporting ABI?  We use
the latest ( 1.11.6 ) for this so I know it does read them and I just
checked with one fresh off a sequencer. But I couldn't find an active
forum for staden.


On Tue, Apr 14, 2009 at 10:20:00AM -0500, Chris Fields wrote:
> For ABI files you'll need an older version of io_lib that supports ABI or 
> the io_lib that comes with the full staden package.  Recent versions of 
> io_lib don't have ABI support built-in anymore.
> chris
> On Apr 14, 2009, at 9:54 AM, Roy Chaudhuri wrote:
>> 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.
>> Roy.
>> 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.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

More information about the Bioperl-l mailing list