[Bioperl-l] Bio::Tools::Glimmer

Chris Fields cjfields at uiuc.edu
Tue Feb 13 15:47:19 EST 2007

You'll also want to update whatever relevant tests there are for  
Glimmer; looks like they are in GenPred.t.


On Feb 13, 2007, at 2:10 PM, Mark Johnson wrote:

>     You're quite correct.  I wasn't paying enough attention.  That  
> does work
> just fine.  I fat-fingered something somewhere else, broke my  
> version of the
> module for GlimmerHMM, hallucinated and confused \S and \s.  8)
>     All I have left now is to fixup the POD documentation and such  
> and then
> I can send the module along and somebody can make whatever tweaks  
> and check
> it in.  Shall I open a ticket in Bugzilla for this and attach  
> diffs, or just
> send them along to somebody to take care of directly?
>     Oh, one thing I have not mentioned.  I also added a -seqname  
> argument.
> Glimmer2 does not provide any kind of sequence identifier in the  
> output, and
> only processes the first sequence in a fasta file.  It would be  
> tedious to
> have to code around this by fixing up the predictions after they are
> produced, so I added the option to provide this missing info up front,
> hopefully allowing downstream code to not have to care as much and  
> have a
> special case for fixing up Glimmer2 predictions.
> On 2/12/07, Torsten Seemann  
> <torsten.seemann at infotech.monash.edu.au> wrote:
>> I think it should be what it says, or perhaps now /^(Glimmer(M| 
>> HMM))/.
>> Here's why:
>> I came onto the scene at Glimmer.pm rev 1.4. At that stage it only
>> parse GlimmerM. I noted that GlimmerHMM was the same output format as
>> GlimmerM, except for the first line. So in rev 1.5 I modified the
>> regexp to match both ie. \S* . This would also hopefully match any
>> other Glimmer-clone formats that arose. I also fixed the pdocs to say
>> this, and added tests to t/Genpred.t.
>> % cvs diff -r 1.4 -r 1.5 Bio/Tools/Glimmer.pm
>> % cvs diff -r 1.15 -r 1.16 t/Genpred.t
>> I then planned to extend support to Glimmer2 and Glimmer3. I added  
>> the
>> 4 test files (t/Glimmer*.out) but never wrote the code. This is where
>> you have come in Mark :-)
>>> I lifted that bit of code to do format detection...we don't have
>> GlimmerHMM
>>> installed locally, so I'm assuming Torsten's output is correct  
>>> and the
>> above
>>> is a bug.  Guess I'll go check bugzilla...
>> I'm pretty sure my 4 test files are correct - I spent a lot of time
>> ensuring they were consistent etc, as I was getting very confused  
>> with
>> the different "glimmer" versions!
>> Hope this all helps,
>> --Torsten
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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