[InterMine Dev] problem building malariamine

Joel Richardson jer at informatics.jax.org
Tue Sep 6 15:21:12 BST 2011


OK, thanks Richard.

On 9/5/11 8:40 AM, Richard Smith wrote:
> Hi Joel,
> I haven't worked out where it went wrong yet but I get the same error
> now on the 0.97 branch. It seems that S is a valid character in a
> FASTA file, I'll update our reverse complement calculation code to
> accept this and several other valid characters;
>
> http://www.bioperl.org/wiki/Reverse_complement
>
> Cheers,
> Richard.
>
>
> On 30/08/2011 16:22, Joel Richardson wrote:
>>
>> Looks like a bug may have been introduced in recent revisions.
>>
>> The 0.97 code that I checked out last week is different from
>> the 0.97 code that Michael checked out in July. Reverting to the
>> older code eliminated the problem.
>>
>> Joel
>>
>> On 8/29/11 4:10 PM, Joel Richardson wrote:
>>> Hi all,
>>>
>>> I'm still stuck on this one. I've checked the malariamine
>>> FASTA files - several do include 'S'. I've also checked the code,
>>> and sure enough, any character that's not a base or N (upper or
>>> lower case) will trigger this exception.
>>>
>>> Can anyone clue me in to what's going on? Thanks!
>>>
>>> Joel
>>>
>>>> On Mon, Aug 29, 2011 at 10:44 AM, Joel Richardson
>>>> <jer at informatics.jax.org <mailto:jer at informatics.jax.org>> wrote:
>>>>
>>>>
>>>> Hi - I'm working through the malariamine tutorial. Everything is
>>>> fine until the postprocessing step. Transfer_sequences dies with
>>>> the following error:
>>>>
>>>> java.lang.__IllegalArgumentException: DNA sequence is invalid -
>>>> cannot contain s
>>>>
>>>> Thanks!
>>>>
>>>> Joel
>>>>
>>>> P.S. Is there a way to search the mailing list archives?
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> ==============================__==============================__===
>>>> Joel Richardson, Ph.D.
>>>> Sr. Research Scientist
>>>> Mouse Genome Informatics
>>>> The Jackson Laboratory Phone: (207) 288-6435
>>>> <tel:%28207%29%20288-6435>
>>>> 600 Main Street Fax: (207) 288-6132 <tel:%28207%29%20288-6132>
>>>> Bar Harbor, Maine 04609 URL: www.informatics.jax.org
>>>> <http://www.informatics.jax.org>
>>>> ==============================__==============================__===
>>>>
>>>> _________________________________________________
>>>> dev mailing list
>>>> dev at intermine.org <mailto:dev at intermine.org>
>>>> http://mail.intermine.org/cgi-__bin/mailman/listinfo/dev
>>>> <http://mail.intermine.org/cgi-bin/mailman/listinfo/dev>
>>>>
>>>>
>>>
>>
>
>
> _______________________________________________
> dev mailing list
> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

-- 

===============================================================
Joel Richardson, Ph.D.
Sr. Research Scientist
Mouse Genome Informatics
The Jackson Laboratory   Phone: (207) 288-6435
600 Main Street          Fax:   (207) 288-6132
Bar Harbor, Maine 04609  URL:   www.informatics.jax.org
===============================================================



More information about the dev mailing list