[Bioperl-l] error parsing new ace files with Bio::Assembly

[Hilmar Lapp]

Possibly useful in addition; posting to the list should reach more, not 
less people though. -hilmar

On Friday, January 24, 2003, at 08:11  AM, Andy Nunberg wrote:

> Should I just e-mail the author of Bio::Assembly instead of posting to 
> the
> list?
> Andy
>> Wed, 22 Jan 2003 11:33:26 -0600
>>
>> Hi,
>> When trying to load ace files using Bio::Assembly i get a number of 
>> errors
>> when calling the next assembly
>> ie
>> $in=Bio::Assembly::IO->new(-file=>$file, -format=>'ace');
>> $assembly=$in->next_assembly;
>> I get several of the following errors
>>
>> Argument "" isn't numeric in numeric comparison (<=>) at
>> /loginhome/anunberg/bioperl-1.2/Bio/SeqFeature/Collection.pm line 436,
>> <GEN0> line 69.
>> At line 69 of my ace file is the quality clipping info eg (QA 81 705 
>> 177
>> 842) which is in the new ace format and not present in the old ace 
>> file
>> format.
>>
>> The new ace format is now considered to be the default format for 
>> phrap.
>>
>> I am using phrap version  0.990319
>>
>> Thanks
>> Andy
>
> *******************************************************************
> Andy Nunberg, Ph.D
> Computational Biologist
> Orion Genomics, LLC
> (314) 615-6989
> http://www.oriongenomics.com
>
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> Bioperl-l at bioperl.org
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>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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