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

[Chris Fields]

Joel,

They haven't stopped supporting it.  IIRC the separate io_lib  
distribution no longer has the ABI headers, but the io_lib with the  
full staden package does (a little confusing, yes).  I have 1.11.6 and  
ABI-related tests for bioperl and bioperl-ext don't pass, but  
compiling with an earlier version does work.  It may be as simple as  
including the header files from an old version, but I haven't tried  
that.

chris

On Apr 15, 2009, at 1:50 AM, Joel Martin wrote:

> Hello,
>   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.
>
> Thanks,
> Joel
>
> 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
>>
>>
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