[Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3
Phillip San Miguel
pmiguel at purdue.edu
Wed Jan 21 22:31:02 UTC 2009
Okay, here are bunch of them:
(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.
> 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.
>> Brian Osborne wrote:
>>> 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
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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