[Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3

Phillip San Miguel pmiguel at purdue.edu
Wed Jan 21 07:45:18 EST 2009


    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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