[Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3

Phillip San Miguel pmiguel at purdue.edu
Wed Jan 21 17:31:02 EST 2009


Okay, here are bunch of them:

http://www.genomics.purdue.edu/~pmiguel/technical/alx/

(Had them on a zip disk...)

phred no longer appears to be able to read them.

Chris Fields wrote:
> Might be worth a try if you can dig any files up.  Frankly if it 
> doesn't work we can probably deprecate that module, unless someone out 
> there managed to get it working.
>
> chris
>
> On Jan 21, 2009, at 6:45 AM, Phillip San Miguel wrote:
>
>>   And the late 90's!
>>   The situation is a little more complex though. Pharmacia had an 
>> older instrument or two called the "Alf" and/or "Alf-red". I never 
>> saw one of those. But the Alfx -- that instrument rocked my world! 
>> 700+ base reads were common and there was a cycle sequencing kit 
>> available so I could sequence off 25+ kb subclones and lambda DNA.
>>   Anyway, I can probably dig up some .alx files. But I think I tried 
>> to read one with SeqIO once and it failed. So it may be that 
>> Bio::SeqIO::alf really only reads the older .alf files, not the more 
>> modern .alx trace file format.
>>   Phred could read them--poorly. It used the raw, rather than the 
>> processed traces, evidently.
>>
>> Phillip
>>
>> Brian Osborne wrote:
>>> Chris,
>>>
>>> This is my doing. Way back when I made an individual test file for 
>>> each SeqIO module, then did my best to find example files for each 
>>> format. I never did find an ALF output file, these machines were 
>>> used in the early '90's.
>>>
>>> Brian O.
>>>
>>> On Jan 18, 2009, at 12:07 AM, Chris Fields wrote:
>>>
>>>> For some reason we have a test suite for Bio::SeqIO::alf but 
>>>> apparently no test data!
>>>
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>>>
>>
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>
>



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