Hilmar Lapp | 1 Dec 07:11 2004
Picon
Picon

Re: AnnotationCollectionI and SeqFeatureI changes


On Monday, November 29, 2004, at 02:24  PM, Allen Day wrote:

>
> primary_tag() and source_tag() being separate from the AC was an 
> oversight
> on my part.  the intention was to move all of the feature's tag 
> attributes
> into the collection.

Honestly, I tend to second Chris' earlier suggestion that this be 
written up in some way. 'This' meaning, what is the targeted behavior 
that you want to become binding for all SeqFeatureI implementations 
that may call themselves compliant. I doubt that a) nobody is confused, 
and that b) everybody is on the same page ...

	-hilmar
--

-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------
Hilmar Lapp | 1 Dec 07:18 2004
Picon
Picon

Re: AnnotationCollectionI and SeqFeatureI changes


On Monday, November 29, 2004, at 01:22  PM, Chris Mungall wrote:

>> It would still require a working XML parser installation, no?
>
> yes - it would require some kind of third-party XML module or modules. 
> I
> guess this may be slightly problemmatic as these are currently all
> optional for bioperl, yep?

Yep.

To me, it's primarily an issue of cross-platform compatibility, unless 
I'm mistaken and there are reasonable pure-perl XML parsers available. 
In my admittedly cursory picture more or less all XML parsers (or those 
of reasonable speed anyway, if the ones frequently used are any 
indication) are based on the expat library. So far I've managed to 
install those modules on all Linux and MacOSX platforms I've worked 
with, sometimes with little and sometimes with a little more trouble, 
but it remains to be seen whether this is an issue for Windows or not.

Anybody out there who can report on installing Expat and XML::Parser 
and friends?

	-hilmar
--

-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------
(Continue reading)

Hilmar Lapp | 1 Dec 07:23 2004
Picon
Picon

Re: AnnotationCollectionI and SeqFeatureI changes

Sounds very reasonable Aaron, and thanks for your gentle herding 
efforts. :-)

For the bioperl developers, this will also mean that for the lifetime 
of the 1.5 branch, efforts should be made to merge fixes applied to the 
HEAD to the branch right afterwards.

	-hilmar

On Monday, November 29, 2004, at 06:07  AM, Aaron J. Mackey wrote:

>
> Yep, OK, I hear you.  I really thought all this was going to be 
> contained to Bio::SeqFeature::Annotated, but I see now that with all 
> sorts of implementation happening in the interfaces (ugh!), this can't 
> happen.  Woe is me.
>
> Here's what I'm willing to do to keep Allen from pulling his hair out: 
> there have been very few changes on the development trunk since RC1 
> that aren't Annotated.pm-related; therefore, (if this makes sense to 
> everyone) I will branch 1.5.0 off of RC1 and merge only those patches 
> that are Annotated.pm-*unrelated* to the 1.5.0 branch.  I will then 
> tag the branch at RC2 (and similarly tag the HEAD, so that any later 
> merging can be done relative to those tags).  Make sense?
>
> Then, the rest of you (Allen, Hilmar, Steffen, etc) need to figure out 
> the cleanest path for 1.6.0, in which all things may change (with an 
> eye towards at least some backwards compatibility); my vote would be 
> that there remain some separation between "heavy" and "light" feature 
> types.  I don't expect/need my Bio::SeqFeature::Simple to implement 
(Continue reading)

Nathan Haigh | 1 Dec 09:35 2004
Picon
Picon

RE: AnnotationCollectionI and SeqFeatureI changes

I'm on WinXP and as far as I remember (or don't remember as the case is), I suspect I mustn't have had too bad a
time installing
them! However I can test this out on a clean Win98 (virtual machine) installation more or less immediately
and if required on a
clean WinXP installation (a bit more hassle and time required for me to do this as I'll have to install WinXP
in a virtual machine).
If all goes smoothly, or has some funny quirks etc, I could write a quick installation guide for BioPerlers
if that's any use!

The only possible problem I can see for the moment is that of the XML::Parser. I'm not sure what version is
installed with
ActiveState, but if BioPerl requires a later version of this module, it can be a bit of a swine to install if
you only use ppm. The
problem is this: if someone tries to update XML-Parser or Compress-Zlib (the latter not used by BioPerl so
shouldn't be a problem)
using ppm from ActiveState Perl on Win95 and Win98, it will do one of two things: 1) either will not update
those modules at all; or
2) will try to update those modules and fail part way through and screw up those modules! The latter being the
worst that can happen
since ppm requires these two modules to function. After this happened with me, I had to do a reinstall of Perl
and all the Perl
modules I had. See http://aspn.activestate.com/ASPN/Downloads/ActivePerl/PPM/ for a few details.

I think all the following XML modules are available as ppd files for ppm installs on windows, as I included
them in a possible
BioPerlv1.5 ppd file:
        XML-DOM
        XML-DOM-XPath
        XML-Node
        XML-Parser
(Continue reading)

Nathan Haigh | 1 Dec 13:21 2004
Picon
Picon

RE: AnnotationCollectionI and SeqFeatureI changes

Which BioPerl test(s) should determine if expat is working correctly?

Nathan

> -----Original Message-----
> From: bioperl-l-bounces <at> portal.open-bio.org [mailto:bioperl-l-bounces <at> portal.open-bio.org]
On Behalf Of Hilmar Lapp
> Sent: 01 December 2004 06:24
> To: Aaron J. Mackey
> Cc: Allen Day; Bioperl
> Subject: Re: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
> 
> Sounds very reasonable Aaron, and thanks for your gentle herding
> efforts. :-)
> 
> For the bioperl developers, this will also mean that for the lifetime
> of the 1.5 branch, efforts should be made to merge fixes applied to the
> HEAD to the branch right afterwards.
> 
> 	-hilmar
> 
> On Monday, November 29, 2004, at 06:07  AM, Aaron J. Mackey wrote:
> 
> >
> > Yep, OK, I hear you.  I really thought all this was going to be
> > contained to Bio::SeqFeature::Annotated, but I see now that with all
> > sorts of implementation happening in the interfaces (ugh!), this can't
> > happen.  Woe is me.
> >
> > Here's what I'm willing to do to keep Allen from pulling his hair out:
(Continue reading)

Brian Osborne | 1 Dec 13:57 2004

RE: AnnotationCollectionI and SeqFeatureI changes

Nathan,

t/Biblio.t is one.

It tests Bio/Biblio/IO/medlinexml.pm, which uses XML::Parser, which uses
expat.

Brian O.

-----Original Message-----
From: bioperl-l-bounces <at> portal.open-bio.org
[mailto:bioperl-l-bounces <at> portal.open-bio.org]On Behalf Of Nathan Haigh
Sent: Wednesday, December 01, 2004 7:21 AM
To: 'Hilmar Lapp'
Cc: 'Bioperl'
Subject: RE: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

Which BioPerl test(s) should determine if expat is working correctly?

Nathan

> -----Original Message-----
> From: bioperl-l-bounces <at> portal.open-bio.org
[mailto:bioperl-l-bounces <at> portal.open-bio.org] On Behalf Of Hilmar Lapp
> Sent: 01 December 2004 06:24
> To: Aaron J. Mackey
> Cc: Allen Day; Bioperl
> Subject: Re: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
>
> Sounds very reasonable Aaron, and thanks for your gentle herding
(Continue reading)

Brian Osborne | 1 Dec 15:07 2004

RE: AnnotationCollectionI and SeqFeatureI changes

Nathan,

I don't know. But if ActiveState can do the equivalent of "force install"
then the answer is "not necessarily".

Brian O.

-----Original Message-----
From: bioperl-l-bounces <at> portal.open-bio.org
[mailto:bioperl-l-bounces <at> portal.open-bio.org]On Behalf Of Nathan Haigh
Sent: Wednesday, December 01, 2004 8:54 AM
To: 'Brian Osborne'; 'Hilmar Lapp'
Cc: 'Bioperl'
Subject: RE: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

Forgive me if I'm being a bit dense! But, if XML::Parser is included in the
ActiveState Perl distribution, doesn't this mean that
expat (or similar) is also installed?

Nathan

> -----Original Message-----
> From: Brian Osborne [mailto:brian_osborne <at> cognia.com]
> Sent: 01 December 2004 12:58
> To: nathanhaigh <at> ukonline.co.uk; 'Hilmar Lapp'
> Cc: 'Bioperl'
> Subject: RE: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
>
> Nathan,
>
(Continue reading)

Nathan Haigh | 1 Dec 14:53 2004
Picon
Picon

RE: AnnotationCollectionI and SeqFeatureI changes

Forgive me if I'm being a bit dense! But, if XML::Parser is included in the ActiveState Perl distribution,
doesn't this mean that
expat (or similar) is also installed?

Nathan

> -----Original Message-----
> From: Brian Osborne [mailto:brian_osborne <at> cognia.com]
> Sent: 01 December 2004 12:58
> To: nathanhaigh <at> ukonline.co.uk; 'Hilmar Lapp'
> Cc: 'Bioperl'
> Subject: RE: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
> 
> Nathan,
> 
> t/Biblio.t is one.
> 
> It tests Bio/Biblio/IO/medlinexml.pm, which uses XML::Parser, which uses
> expat.
> 
> Brian O.
> 
> 
> -----Original Message-----
> From: bioperl-l-bounces <at> portal.open-bio.org
> [mailto:bioperl-l-bounces <at> portal.open-bio.org]On Behalf Of Nathan Haigh
> Sent: Wednesday, December 01, 2004 7:21 AM
> To: 'Hilmar Lapp'
> Cc: 'Bioperl'
> Subject: RE: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
(Continue reading)

Affan Qureshi | 1 Dec 15:19 2004

Discovering new genes

Hi,
This is a newbie question, maybe not directly related to BioPerl even.

I am a student working on a set of newly discovered DNA sequence files for
an organism. I would like to know the steps involved in discovering and
analyzing the DNA sequences. I want to classify the various functional
units in the genes represented by the DNA sequences.

I have conducted a Blastx search for all the 100 files and have found some
very good matches (e.g e-value 1e-120). I have seperated out the big match
sequences in a seperate file. I want to know what the next steps are.
Maybe I should compare the matched sequences(proteins) against the
corresponding ones in other organisms like Yeast, worm, drosophila etc and
find out whether there is a similarity between the neighboring proteins. I
tried doing this at SPRING website and looked up the matches on SWISS-PROT
etc.

I thought since you guys are experienced bioinformaticists and do this
type of work every day, maybe you could give me some pointers.

Sorry about the off-topic question.

Thanks,

Affan
Nathan Haigh | 1 Dec 15:52 2004
Picon
Picon

RE: AnnotationCollectionI and SeqFeatureI changes

ActiveState Perl has a module called XML::Parser::expat. Could this be a perl implementation of the expat library?

Nathan

> -----Original Message-----
> From: Brian Osborne [mailto:brian_osborne <at> cognia.com]
> Sent: 01 December 2004 14:08
> To: nathanhaigh <at> ukonline.co.uk; 'Hilmar Lapp'
> Cc: 'Bioperl'
> Subject: RE: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
> 
> Nathan,
> 
> I don't know. But if ActiveState can do the equivalent of "force install"
> then the answer is "not necessarily".
> 
> Brian O.
> 
> -----Original Message-----
> From: bioperl-l-bounces <at> portal.open-bio.org
> [mailto:bioperl-l-bounces <at> portal.open-bio.org]On Behalf Of Nathan Haigh
> Sent: Wednesday, December 01, 2004 8:54 AM
> To: 'Brian Osborne'; 'Hilmar Lapp'
> Cc: 'Bioperl'
> Subject: RE: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
> 
> 
> Forgive me if I'm being a bit dense! But, if XML::Parser is included in the
> ActiveState Perl distribution, doesn't this mean that
> expat (or similar) is also installed?
(Continue reading)


Gmane