[Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3

Chris Fields cjfields at illinois.edu
Wed Jan 21 07:59:19 EST 2009


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!
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



More information about the Bioperl-l mailing list