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Sendu Bala | 1 Mar 01:13
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Re: Issues with new Bio::Tools::Run modules for Genemark and Glimmer

Mark Johnson wrote:
> I'm using _rearrange() now.  I'll look at _set_from_args().  Is either one
> preferred to the other?

_set_from_args() is implemented using _rearrange() iirc. In any case, 
they do different things but _set_from_args() just makes creating 
wrapper modules a lot simpler. Another example: compare revisions 1.15 
and 1.16 of Bio::Tools::Run::Alignment::Lagan where I reimplemented it 
to use _set_from_args() and _setparams().

http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-run/Bio/Tools/Run/Alignment/Lagan.pm.diff?r1=text&tr1=1.15&r2=text&tr2=1.16&diff_format=h

So, its new, but I'd recommend new modules, especially wrappers, make 
use of it.
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Sendu Bala | 1 Mar 01:19
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Re: Problem of Installing Bioperl

Chan Kuang Lim wrote:
> I have problem of installing bioperl in windows using command-line installation.
> In the cmd windows, after 
> ppm-shell
> search bioperl
> install 2
> 
> many downloading had done, but the next line is:
> Unpacking bioperl-1.5.2_100...ppm install failed: Can't extract files from C:.............../Bioperl-1.5.2_100.tgz

Does that file exist on your system? Is it larger than 0kb? Can you open 
it yourself?
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Chris Fields | 1 Mar 02:19
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Re: Issues with new Bio::Tools::Run modules for Genemark and Glimmer


On Feb 28, 2007, at 6:13 PM, Sendu Bala wrote:

> Mark Johnson wrote:
>> I'm using _rearrange() now.  I'll look at _set_from_args().  Is  
>> either one
>> preferred to the other?
>
> _set_from_args() is implemented using _rearrange() iirc. In any case,
> they do different things but _set_from_args() just makes creating
> wrapper modules a lot simpler. Another example: compare revisions 1.15
> and 1.16 of Bio::Tools::Run::Alignment::Lagan where I reimplemented it
> to use _set_from_args() and _setparams().
>
> http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-run/Bio/Tools/Run/ 
> Alignment/Lagan.pm.diff? 
> r1=text&tr1=1.15&r2=text&tr2=1.16&diff_format=h
>
> So, its new, but I'd recommend new modules, especially wrappers, make
> use of it.

Agreed; I think it allows for parameter variations (dashed, dashless,  
etc) and can create on-the-fly simple get/setters, so is particularly  
suited for wrappers.

_rearrange() will always have use in situations where using named  
parameters helps (long arg lists) but you don't want get/setters,  
just values.
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Dave Messina | 1 Mar 02:40
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Re: Problem installing bioperl-1.5.2_102

> t/compat.t     5  1280    60    5   8.33%  25-28 31

This is the test that failed. I think you snipped the part above where the
actual errors causing the failure was printed.

> There seems to be running another CPAN process (pid 7207). Contacting...
> Lockfile /Users/sand60/.cpan/.lock not writeable by you. Cannot proceed.
>     On UNIX try:
>     rm /Users/sand60/.cpan/.lock
>   and then rerun us.
>  at -e line 1
> ###################################################
> And doing what it says, removing some lock file doesn't help.

Are you sure the lock file is really being removed? If so, what was the
error you got when running it after doing that?

Also, this line is important:
>  /usr/bin/make test -- NOT OK

It looks like you're trying to install on OS X. By default, OS X has perl
but not make. So /usr/bin/make probably doesn't exist on your system,
along with lots of other UNIX tools you'll want. To verify this, type:

which /usr/bin/make

on the command line. If you get:
/usr/bin/make: Command not found.

you'll need to install the OS X developer tools, called Xcode. You'll need
(Continue reading)

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Hilmar Lapp | 1 Mar 05:16
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Re: Issues with new Bio::Tools::Run modules for Genemark and Glimmer


On Feb 28, 2007, at 5:54 PM, Mark Johnson wrote:

> I don't like using system() due to issues with
> signals (Such as the user hitting ctrl-c and taking out the  
> child).  I feel
> better knowing the wrapped executable is in another process  
> disconnected
> from the console.

I'm not sure how the user would be able to take out the child hitting  
ctrl-c if you run it through system() (except if the parent  
terminates first - but maybe then terminating a run-away child is in  
good order).

I haven't read the IPC::run POD in full detail but you will want to  
make sure that if the parent gets killed the child does get killed  
too, or otherwise you'll have a run-away process that novices will  
have trouble with understanding or terminating.

Other than that though IPC::run seems like a useful module, so  
incurring this as a dependency should be fine.

	-hilmar
--

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================
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Samuel GRANJEAUD - IR/IFR137 | 1 Mar 08:36
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Re: retrieven ids

Hi,

I am not sure it's the key answer but the FAQ may help you

http://www.bioperl.org/wiki/FAQ#How_do_I_retrieve_a_nucleotide_coding_sequence_when_I_have_a_protein_gi_number.3F

Cheers,
--Samuel

Luba Pardo wrote:
> Hi everyone,
> I wonder if someone could give an advice of the following:
> I want to retrieve the DNA coding sequence of a RefSeq protein id. I do not
> want to translate the protein back to DNA, but rather get the DNA coding
> sequence ID and then retrieve the DNA sequence from Gen Bank. Is there any
> module that allow to get all possible ids for a sequence given a gi protein
> ?
>
> Thank you very much in advance,
> L. Pardo
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
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Luba Pardo | 1 Mar 08:48
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Re: retrieven ids

Thank you very much.
L. Pardo

On 28/02/07, Dave Messina <dmessina <at> wustl.edu> wrote:
>
> Whenever I'm unsure of how to do something, I first look to see if one of
> the  HOWTOs on bioperl.org covers it. In this case, the Features HOWTO has
> example code which I think will do what you want.
>
> Genbank records typically have the coding sequence of a protein as a
> feature, so I would do something like:
>
> - use the RefSeq protein IDs to query Entrez and get back the Genbank
> records.
>
> - read the Features HOWTO to refresh my memory on the syntax for grabbing
> features.
>
> That HOWTO is at:
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
>
> - whip up a little script to loop through the Genbank records one at a
> time with SeqIO and pull out the cDNA sequence features.
>
>
> Dave
>
>
>
(Continue reading)

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Samuel GRANJEAUD - IR/IFR137 | 1 Mar 11:09
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Re: _rearrange

Hi,

May be you will find information in

http://www.bioperl.org/wiki/Advanced_BioPerl#rearrange.28.29

http://www.bioperl.org/wiki/Bioperl_Best_Practices

Cheers,
--Samuel

Caroline Johnston wrote:
> hi,
>
> Is there a discussion of the rationale behind the _rearrange method
> somewhere? I'm probably just being gormless, but I think I'm missing the
> point a bit.
>
> Is it okay for a method just to expect named params like
> ->foo(arg1=>'stuff', arg2=>'things'); ?
>
> Cxx
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
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michael watson (IAH-C | 1 Mar 11:58
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Re: The axis of GC content in Bio::Graphics::glyph:dna

In fact, those pad_left and pad_right arguments have no effect
whatsoever (using bioperl 1.5.2_100)

 my $panel = Bio::Graphics::Panel->new(-key_style => between,
     -offset    => $start,
     -length    => $stop - $start + 1,
     -width     => 800
     -pad_left =>5000,
     -pad_right =>5000
     );

Even if I set them to 5000, the image looks exactly as if I had not set
them.

The only way I can get around this is to edit Glyph/dna.pm lines 184 and
186 such that $x2+3 is changed to $x2-20 - then the axes are drawn on
the image instead of outside of it.   This is obviously a hack, which
upsets my karma.

Mick

________________________________

From: lincoln.stein <at> gmail.com [mailto:lincoln.stein <at> gmail.com] On Behalf
Of Lincoln Stein
Sent: 15 February 2007 18:53
To: michael watson (IAH-C)
Cc: BioPerl-List
Subject: Re: [Bioperl-l] The axis of GC content in
Bio::Graphics::glyph:dna
(Continue reading)

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michael watson (IAH-C | 1 Mar 12:01
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Re: The axis of GC content in Bio::Graphics::glyph:dna

On further inspection, the lack of a comma was causing my karma upset -
apologies.

Mick

________________________________

From: michael watson (IAH-C) 
Sent: 01 March 2007 10:58
To: 'lincoln.stein <at> gmail.com'
Cc: BioPerl-List
Subject: RE: [Bioperl-l] The axis of GC content in
Bio::Graphics::glyph:dna

In fact, those pad_left and pad_right arguments have no effect
whatsoever (using bioperl 1.5.2_100)

 my $panel = Bio::Graphics::Panel->new(-key_style => between,
     -offset    => $start,
     -length    => $stop - $start + 1,
     -width     => 800
     -pad_left =>5000,
     -pad_right =>5000
     );

Even if I set them to 5000, the image looks exactly as if I had not set
them.

The only way I can get around this is to edit Glyph/dna.pm lines 184 and
186 such that $x2+3 is changed to $x2-20 - then the axes are drawn on
(Continue reading)

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Gmane