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

Mark Johnson johnsonm at gmail.com
Tue Feb 13 15:10:23 EST 2007


    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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