Koen van der Drift | 1 Feb 18:08 2004
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Re: Bio::UnivAln mourned

> But I just migrated from linux to OS X, and my latest install (bioperl
> 1.4)
> was virgin to my new machine.
>
> After my scripts carped I placed UnivAln.pm from an old bioperl dist (I
> used 0.7.0)
> into my bioperl-1.x build tree (install-dist/Bio) and added it's name
> to my MANIFEST
> before running (or re-running) perl Makefile.PL.
>
> Now it works without apparent conflicts in my set-up, YMMV.
>
> I understand that maybe the demise of the module is due to its lack of
> a maintainer keeping its
> guts up-to-date with bioperl root structure. I would perhaps be willing
> to help here.
> Would there be objections to its revival? Or are there plans to expand
> existing modules?

Hi,

I am the current maintainer of the fink package for bioperl. I have 
already submitted the new version (1.4) to fink a few weeks ago. 
Unfortunately, the powers that be have not yet put the package into the 
fink cvs, so it is not yet available. The fink team is currently 
restructuring the way perl modules get installed, and it seems that the 
bioperl package is on hold until this is resolved. If you want I can 
mail you the info file for bioperl offlist, so you can use it with 
fink.

(Continue reading)

Lincoln Stein | 2 Feb 10:07 2004

Re: Filehandle interface in Bio::AlignIO: broken in 1.4?

So sorry about breaking the newFh method.  You can restore the 
previous behavior by passing \*ARGV to the -fh argument when you 
create the SeqIO object.

Unfortunately the earlier behavior made it impossible to  create a 
seqIO object that was write only, and as a result some higher-level 
modules were gobbling the STDIN inappropriately.

Lincoln

On Saturday 31 January 2004 05:07 pm, Jason Stajich wrote:
> Dave -
>
> This is due to a change lincoln made to not default to the magic <>
> operator when no filename is provided.  It broke a lot of my
> scripts too.
>
> [This is basically part of similar question that Peter was asking
> wrt SeqIO]
>
> I would like to see it come back somehow but I am not sure how as
> it causes certain things to block during the tests.
>
> it has nothing to do with the newFh method but with Bio::Root::IO
> in the _readline method.
>
> <     my $fh = $self->_fh || \*ARGV;
> ---
>
> >     my $fh = $self->_fh or return;
(Continue reading)

Bernhard Schmalhofer | 2 Feb 10:15 2004
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Re: Testing BioPerl objects for equality

Ewan Birney wrote:
> 
> On Thu, 29 Jan 2004, Peter van Heusden wrote:
> 
> 
>>I've got an idea for testing where I'd like to 'round-trip' through
>>SeqIO: read in from a file on disk, write out again with write_seq() and
>>then read in the file written by write_seq() and compare the two
>>sequence objects. If they aren't equal, it means we've got a problem.
> 
> 
> That sounds like a great idea... we've always had problems with diff'ing
> the files because of whitespace issues, but diff'ing the objects sounds
> great.
> 
> 
>>To make this work requires some kind of equals() method on Seq,
>>SeqFeature, etc. This doesn't seem to be there at the moment - or am I
>>missing something? Maybe there should probably be some kind of
>>Bio::ComparableI interface which provides an equals() abstract method.
>>
> 
If the roundtrip is starting from a file is a specific format, shouldn't 
it be possiple to compare the data structures of the sequence object 
directly?
I was think of using something like Test::More::is_deeply(), which tells 
you where the data structures start to become different.

CU, Bernhard
--

-- 
(Continue reading)

Heikki Lehvaslaiho | 2 Feb 12:41 2004
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working with large alignments


Albert Vilella who is visiting me here at EBI works with really big genomic 
sequence alignments. I've committed several of his modules into cvs for that 
purpose. The most important additions are:

* Bio::Seq::LargeLocatableSeq
    Bio::RangeI compliant Bio::Seq::LargePrimarySeq 
    uses File::Tmp for seq storing
* Bio::Seq::LargeSeqI
    Interface class for LargeSeq implemantations
* Bio::AlignIO::largemultifasta
    IO class creating Bio::Seq::LargeLocatableSeq and SimpleAlign objects

The LargeLocatableSeq is based on code from Bio::Seq::LargePrimarySeq. 
Everything seems to work but if we run tests added to the end of the 
t/AlignIO.t file with larger files, the process is still using large amount 
of memory. We'be interested from hearing from anyone who can suggest 
improvements.

You are willling to test the code with larger data sets, I've put two files 
here:

http://www.ebi.ac.uk/~lehvasla/bioperl/medium.largemultifasta (1.3M)
http://www.ebi.ac.uk/~lehvasla/bioperl/large.largemultifasta (31M)

Thanks,

	-Heikki  and Albert
--

-- 
______ _/      _/_____________________________________________________
(Continue reading)

matthieu CONTE | 2 Feb 13:11 2004
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Re: Bio ::seqIO ::tigr


Ok...
But the method “get_BioDatabaseAdaptor” doesn't exist in the
Bio::DB::BioSQL::DBAdaptor module (documentation). I didn't find it on the 
bioperl-db web  page
    Any idea ?

Thanks

Matthieu CONTE
M. Sc. in Bioinformatics from SIB

00 33 06.68.90.28.70
m_conte <at> hotmail.com

>From: Hilmar Lapp <hlapp <at> gmx.net>
>To: "matthieu CONTE" <m_conte <at> hotmail.com>
>CC: bioperl-l <at> bioperl.org
>Subject: Re: [Bioperl-l] Bio ::seqIO ::tigr
>Date: Wed, 28 Jan 2004 08:55:15 -0800
>
>I suspect you have an old version of bioperl-db, or a version mix-up. You 
>need to download and install the latest revision from CVS for bioperl-db.
>
>Note that if the root of the problem is with the pir parser then 
>load_seqdatabase.pl will not cure it, as it just uses any Bio::SeqIO 
>compliant parser to provide the input sequences. If the parser is broken 
>then there won't be input ... It just saves you the round-trip (and 
>possible errors associated with it) of going through swissprot format.
>
(Continue reading)

Hilmar Lapp | 2 Feb 16:55 2004
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Re: Bio ::seqIO ::tigr

That's why I said you seem to have a version mix-up in addition.  
get_BioDatabaseAdaptor is part of the 0.1 API, which was retired more  
than a year ago.

	-hilmar

On Monday, February 2, 2004, at 04:11  AM, matthieu CONTE wrote:

>
> Ok...
> But the method “get_BioDatabaseAdaptor” doesn't exist in the
> Bio::DB::BioSQL::DBAdaptor module (documentation). I didn't find it on  
> the bioperl-db web  page
>    Any idea ?
>
> Thanks
>
>
>
> Matthieu CONTE
> M. Sc. in Bioinformatics from SIB
>
> 00 33 06.68.90.28.70
> m_conte <at> hotmail.com
>
>
>
>
>
>> From: Hilmar Lapp <hlapp <at> gmx.net>
(Continue reading)

James Mitchell | 2 Feb 22:45 2004

Bio::Ontology - parsing GO files

I'm using Bio::Ontology modules to access GO tree information, ie.
ancestors/descendants of a given node.  I'm using it like this:
---
use strict;
use Bio::Ontology::SimpleGOEngine;

my $gendir = $ENV{GeneLink_Dir};
my $deffile = $gendir . "GO.defs";
my $comfile = $gendir . "component.ontology";
my $funfile = $gendir . "function.ontology";
my $profile = $gendir . "process.ontology";
my $parser = Bio::Ontology::SimpleGOEngine->new
	( -defs_file => $deffile,
	  -files     => [$comfile,
	                 $funfile,
	                 $profile] );
my $engine = $parser->parse();
---
I'm getting this error though:
Can't locate object method "parse" via package
"Bio::Ontology::SimpleGOEngine" (
perhaps you forgot to load "Bio::Ontology::SimpleGOEngine"?)
---
Is this the correct method for parsing GO files?  I'm using version 1.4 on
Windows.

thanks,
James
Help | 3 Feb 09:45 2004

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I took the only one pijll of Cialjs and that was such a GREAT weekend!
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Cbalis- it`s COOL!!! The best weekend stuff I've ever trhied!
Haven`t you tried yet?

DO IT NkOW at 
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Hilmar Lapp | 3 Feb 07:32 2004
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Re: Bio::Ontology - parsing GO files


On Monday, February 2, 2004, at 01:45  PM, James Mitchell wrote:

> my $parser = Bio::Ontology::SimpleGOEngine->new
>

Is this still in the documentation? If so, I apologize. You parse 
ontologies analogous to other IO APIs in bioperl:

	$ont_stream = Bio::OntologyIO->new(-format => 'go',
                                         -files => [....],
                                         -defs_file => $deffile);

and then

	while(my $ont = $ont_stream->next_ontology()) {
		# do something with $ont (it's a Bio::Ontology::OntologyI)
	}

Most ontology streams will only have one ontology ever. So, for GO you 
could as well say

	my $go_ont = $ont_stream->next_ontology();

Hth,

	-hilmar

--

-- 
-------------------------------------------------------------
(Continue reading)

Lincoln Stein | 3 Feb 10:37 2004

Re: Testing BioPerl objects for equality

I think that's a great idea.  I hadn't known about test_deeply().  
There's also a Test::Differences module, that does something similar.

Lincoln

On Monday 02 February 2004 11:15 am, Bernhard Schmalhofer wrote:
> Ewan Birney wrote:
> > On Thu, 29 Jan 2004, Peter van Heusden wrote:
> >>I've got an idea for testing where I'd like to 'round-trip'
> >> through SeqIO: read in from a file on disk, write out again with
> >> write_seq() and then read in the file written by write_seq() and
> >> compare the two sequence objects. If they aren't equal, it means
> >> we've got a problem.
> >
> > That sounds like a great idea... we've always had problems with
> > diff'ing the files because of whitespace issues, but diff'ing the
> > objects sounds great.
> >
> >>To make this work requires some kind of equals() method on Seq,
> >>SeqFeature, etc. This doesn't seem to be there at the moment - or
> >> am I missing something? Maybe there should probably be some kind
> >> of Bio::ComparableI interface which provides an equals()
> >> abstract method.
>
> If the roundtrip is starting from a file is a specific format,
> shouldn't it be possiple to compare the data structures of the
> sequence object directly?
> I was think of using something like Test::More::is_deeply(), which
> tells you where the data structures start to become different.
>
(Continue reading)


Gmane