[InterMine Dev] problem building malariamine

Richard Smith richard at flymine.org
Mon Sep 5 13:40:12 BST 2011


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>
>>> ==============================__==============================__===
>>>
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>>>
>>>
>>
>




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