headers
Jason Stajich | 1 Sep 2003 04:28

Re: ace to msf format?

Each Contig is a Bio::Align::AlignI - so in theory you can manipulate
them as if they are Bio::SimpleAlign objects.  Robson can clarify if there
are any caveats there.

But you want to do this to have access to each contig in the scaffold:
foreach my $contig ( $scaffold->all_contigs ) {
 # process Bio::Assembly::Contig object here
}

Your code below is calling it in scalar context which will just have $aln
being set to the length of the returned array.

-jason

On Mon, 1 Sep 2003, Wes Barris wrote:

> Brian Osborne wrote:
>
> > Wes,
> >
> > I don't think this is possible in Bioperl. To put it more generally, AlignIO
> > can't accommodate Assembly objects currently. AlignIO is the module that
> > takes in a variety of alignment formats and interconverts them, analogous to
> > SeqIO. I'll be corrected if I'm wrong.
> >
> > Brian O.
>
> I am kind of new to this so I could be wrong but isn't an Assembly a group
> of alignments?  So, from one assemble, a group of alignments could be
> generated?
(Continue reading)

Permalink | Reply | 4 comments |
headers
Wes Barris | 1 Sep 2003 07:29
Picon
Picon
Favicon

Re: ace to msf format?

Jason Stajich wrote:

> Each Contig is a Bio::Align::AlignI - so in theory you can manipulate
> them as if they are Bio::SimpleAlign objects.  Robson can clarify if there
> are any caveats there.
> 
> 
> But you want to do this to have access to each contig in the scaffold:
> foreach my $contig ( $scaffold->all_contigs ) {
>  # process Bio::Assembly::Contig object here
> }

Thanks Jason, that makes sense.  Perhaps I'm missing something obvious
but I am getting an error when treating each contig as a Bio::SimpleAlign
object.  Here is my code:

#!/usr/local/bin/perl -w
#
use strict;
use Bio::Assembly::IO;
use Bio::AlignIO;
#
my $usage = "Usage: $0 <infile.ace>\n";
my $infile = shift or die $usage;

my $io = new Bio::Assembly::IO(-file=>$infile, -format=>'ace');
my $assembly = $io->next_assembly;

foreach my $contig ($assembly->all_contigs()) {
    my $name = "cn".$contig->id;
(Continue reading)

Permalink | Reply | 3 comments |
headers
Flywheel | 1 Sep 2003 04:41
Picon
Favicon

Re: How Energy Storage can help us ?


Nice Hello from Flywheel Storage 

& Sun Tracking 

Goodbay to Blackout forever 

rysz_c2 <at> yahoo.com

Responding to your Questions;

We offer Safety Solution

Rolling Blackout will always happened, since the SYSTEM - 
is design to protect itself in dangerous 
Over-Current Situations.

Breakers basic duty is defense whole system, shut down, 
and isolate from Grid; 

"Wave of over-current" travel to next Sub-Station
and stimulate the same results on another, then another, 
then another. And a VOLTAGE is growing rapidly.

Growing Disconnection in Domino Effect; 
we did seen twice;

Accident ~ 30 years ago (baby boom) - for purpose recently.

To decrease all "Over-Current situation"
(Continue reading)

Permalink | Reply | 0 comments |
headers
Flywheel | 1 Sep 2003 04:41
Picon
Favicon

Re: How Energy Storage can help us ?


Nice Hello from Flywheel Storage 

& Sun Tracking 

Goodbay to Blackout forever 

rysz_c2 <at> yahoo.com

Responding to your Questions;

We offer Safety Solution

Rolling Blackout will always happened, since the SYSTEM - 
is design to protect itself in dangerous 
Over-Current Situations.

Breakers basic duty is defense whole system, shut down, 
and isolate from Grid; 

"Wave of over-current" travel to next Sub-Station
and stimulate the same results on another, then another, 
then another. And a VOLTAGE is growing rapidly.

Growing Disconnection in Domino Effect; 
we did seen twice;

Accident ~ 30 years ago (baby boom) - for purpose recently.

To decrease all "Over-Current situation"
(Continue reading)

Permalink | Reply | 1 comment |
headers
Heikki Lehvaslaiho | 1 Sep 2003 11:48
Picon
Picon
Favicon

Re: bugs on branch; tests on main trunk

On Fri, 2003-08-29 at 17:56, Ewan Birney wrote:
> I have fixed the translate() and pdb res bug on the branch.
> 
Great.

> Heikki or Rob --- does RestrictionEnzyme *really* need Storeable?
> Storeable doesn't come by default on systems, so if it didn't need
> it then it would be more useful not to use it. Any chance of this?

Storable is used to do deep cloning of Enzyme objects. Storable is also
used by Bio::DB::FileCache and Bio::SeqFeature::Collection (or is the
documentation for Collection outdated?). 

Storable is part of 5.8.1 distribution. There is Clone in CPAN which is
faster but less systems are bound to have is.

If you think is is critical to get rid of this dependency I can rewrite
the cloning method.

	-Heikki

> 
> I put a require eval() in tutorial around the restriction enzyme stuff.
> 
> 
> 
> 
> Chris (and the unflattening crew...) the Unflattener is issueing alot of
> warnings with -w --- any chance of one of you looking at it?
>
(Continue reading)

Permalink | Reply | 5 comments |
headers
Heikki Lehvaslaiho | 1 Sep 2003 12:21
Picon
Picon
Favicon

Re: doing a 1.2.3 release

I am here!  Two week without email on holiday needs one week to sort
things out. I am ~ ready again.

Jason, Can you do the supervise the 1.2.3 release?

I'll start looking into 1.3/1.4.  I'll post an other message to start a
new thread on it.

	-Heikki 

On Fri, 2003-08-29 at 17:50, Ewan Birney wrote:
> On Fri, 29 Aug 2003, Lincoln Stein wrote:
> 
> > What are the timetables for 1.2.3 and 1.3?
> >
> 
> 
> 1.2.3 soon(ish)
> 
> 1.3 Heikki should decide. I am not on campus at the moment, so will try to
> track him down next week...
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
--

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
(Continue reading)

Permalink | Reply | 0 comments |
headers
Heikki Lehvaslaiho | 1 Sep 2003 12:49
Picon
Picon
Favicon

planning for bioperl 1.4


Summer is over and it is time to start preparing next major release of
bioperl which will be release 1.4.

Before it is out there will be a series of tarballed development
releases named 1.3.0, 1.3.1, 1.3.2, ... We will tag them in the cvs head
but will not branch until 1.4.0 release.

First, we need to get a clearer picture what has been added into bioperl
since 1.2 release was made at the end of year 2002. Please, add them
into Changes file in the CVS head. Never mind the format, we can sort
that out later. I'll go through news to see what major additions there
have been.

Secondly, all developers, please post here about projects you'd like to
finish before the release and your estimate when it would be ready for
release.

Depending on those comments, we can readjust the release schedule but
I'd like to see first 1.3.X out in a month (some time after 1.2.3) and
1.4 in two months at most. 

	-Heikki

--

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
(Continue reading)

Permalink | Reply | 0 comments |
headers
Markus Kador | 1 Sep 2003 16:19
Picon

GeneDB Question

Hi,

I would like to get sequence data form GeneDB (http://www.genedb.org/) 
in my perl script.
Since there is no module available I wanted to ask if anyone has ever 
done that or has any pointers on how to achive that. Specifically the 
blast server would be interesting.

Thanks in advance,

Markus
Permalink | Reply | 2 comments |
headers
Keith James | 1 Sep 2003 18:47
Picon
Favicon

Re: GeneDB Question

>>>>> "Markus" == Markus Kador <markus <at> kador.de> writes:

    Markus> Hi, I would like to get sequence data form GeneDB
    Markus> (http://www.genedb.org/) in my perl script.  Since there
    Markus> is no module available I wanted to ask if anyone has ever
    Markus> done that or has any pointers on how to achive
    Markus> that. Specifically the blast server would be interesting.

As I'm at Sanger I've just been round to the genedb office to ask
about this.

I think that you will have to try screen-scraping the omniblast page
(rather than the individual organism blast pages). This way you can
search all the data but only have to maintain your script to mirror
the changes to one submission web page. However, that page is subject
to periodic changes in formatting and in the number and labelling of
radio buttons and checkboxes.

As you know, there is no public server or API. There is no likelihood
of these becoming available in the forseeable future, so a web-scraper
may be worth the effort.

I also asked about ftp availability of the data because I think that
if you have the resources (disk space & local blast) your best option
is to ftp the data to your local machine. Due to ongoing data-release
policy issues the ftp site data is not complete for some
organisms. You would need to contact the genedb people directly about
that.

HTH
(Continue reading)

Permalink | Reply | 1 comment |
headers
Lincoln Stein | 2 Sep 2003 00:18
Favicon

Re: Bio::Graphics::Panel, -spacing => 0 constructor problem.

Spacing adds additional padding between tracks.  You cannot get them to overly 
each other.  Possibly -start and -end are not doing what you think they 
should do.

Lincoln

On Friday 22 August 2003 06:23 pm, Philip MacMenamin wrote:
> Hi,
>
> Am I right in thinking that the '-spacing' constructor for
> Bio::Graphics::Panel, if set to 0, should result in no space between
> tracks? ie That the tracks are either over-laying eachother, or squashed
> down onto the same plane as the previous one.
>
> I cannot get this to happen if this is its purpose. It continues to stack
> the tracks on the panel as per default. (So I have left it out, its not
> useful to see this). I know that it works, because I have seen it working
> in the wormbase UTRs.
>
> Here is some code:
> #   if (scalar  <at> threePrimeUTR >0)
> #    {
> #      $panel->add_track(generic=>\ <at> threePrimeUTR,
> #			-bgcolor      => 'lightblue',
> #			-fgcolor      => 'black',
> #		#	-bump      =>  +1,
> #			-spacing => 0,
> #			-utr_color    => '#D0D0D0', ##whats this about?, chnging makes no dif?
> #			-font2color   => 'blue',
> #			-height       => 10,
(Continue reading)

Permalink | Reply | 2 comments |

Gmane