[Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3

Chris Fields cjfields at illinois.edu
Sat Feb 21 17:05:44 EST 2009

Patches are always welcome.  ;>


On Feb 21, 2009, at 3:31 PM, Martin MOKREJŠ wrote:

> For the completeness of the archives, it seems there used to
> be a Gelminder tool to read gel files.
> I cannot find anymore other sources than a backup of RCS files.
> But somebody more skilled is probably able to recreate the
> sources from the RCS-generated diffs.
> ftp://ftp.sanger.ac.uk/pub/badger/gelminder
> ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/gelminder/
> ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/gelmover/
> For sure that should be helpful to somebody having the time
> to read in the sources how to interpret the file format.
> Not my case, though. ;)
> Martin
> Phillip San Miguel wrote:
>> 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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