[Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3

[Martin MOKREJŠ]

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!