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Chris Fields | 3 Sep 01:54
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(no subject)

Posted this to biosql-l already but felt it needed posting here as  
well.  Sorry if you get this twice.

I noticed some critical recursion issues with bioperl-db when working  
in Bio::Ontology changes.  This was using bioperl-live (post-feature/ 
annotation fixes).  Bug report is here:

http://bugzilla.open-bio.org/show_bug.cgi?id=2355

It seems to be Bio:Taxon related; this is from 03swiss.t:

--------------------- WARNING ---------------------
MSG: recursion detected for Bio::Taxon object
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:681
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:630
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:692
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:630
...
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:587
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
(Continue reading)

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Chris Fields | 3 Sep 01:57
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recursion issues with bioperl-db

Apologies if you get this more than once; the first post appeared to  
get sent w/o a proper subject line.  Posted this to biosql-l already  
but felt it needed posting here as well.

I noticed some critical recursion issues with bioperl-db when working  
in Bio::Ontology changes.  This was using bioperl-live (post-feature/ 
annotation fixes).  Bug report is here:

http://bugzilla.open-bio.org/show_bug.cgi?id=2355

It seems to be Bio:Taxon related; this is from 03swiss.t:

--------------------- WARNING ---------------------
MSG: recursion detected for Bio::Taxon object
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:681
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:630
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:692
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:630
...
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:587
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
(Continue reading)

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Chris Fields | 3 Sep 03:40
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Re: recursion issues with bioperl-db

Okay, we can the previous posts!  Odd, but I started from scratch and  
can't reproduce the issue; there may have been some cross-talk with  
different bioperl installations on my laptop.  Anyway, everything  
passes now w/o recursion so I'll mark the bug as invalid.

chris

On Sep 2, 2007, at 6:57 PM, Chris Fields wrote:

> Apologies if you get this more than once; the first post appeared to
> get sent w/o a proper subject line.  Posted this to biosql-l already
> but felt it needed posting here as well.
>
> I noticed some critical recursion issues with bioperl-db when working
> in Bio::Ontology changes.  This was using bioperl-live (post-feature/
> annotation fixes).  Bug report is here:
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=2355
>
> It seems to be Bio:Taxon related; this is from 03swiss.t:
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child
> /Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:681
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent
> /Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:630
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child
(Continue reading)

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Bernd Web | 3 Sep 14:43
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Fh::flush warning

Hi,

Sometimes with Bio::SimpleAlign/AlignIO, I get the following warning:
(in cleanup) Undefined subroutine Fh::flush, at
/lib/perl/Bio/Root/IO.pm line 541.

This occurs in a rather large script and have not been able to isolate
a small example where I also get this warning. Does someone know more
about this warning and why it is thrown?

Regards,
Bernd
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Chris Fields | 3 Sep 16:41
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Re: Fh::flush warning

Could you give a bit more info (bioperl version, OS, etc)?

I'm guessing a recent version as the error coincides with a call to  
flush() in Root::IO (which is probably called indirectly via DESTROY)  
and that you're probably using a tied filehandle somewhere for  
output, e.g. Bio::AlignIO::newFh() or Bio::AlignIO::fh(), so knowing  
the input/output formats could help.

chris

On Sep 3, 2007, at 7:43 AM, Bernd Web wrote:

> Hi,
>
> Sometimes with Bio::SimpleAlign/AlignIO, I get the following warning:
> (in cleanup) Undefined subroutine Fh::flush, at
> /lib/perl/Bio/Root/IO.pm line 541.
>
> This occurs in a rather large script and have not been able to isolate
> a small example where I also get this warning. Does someone know more
> about this warning and why it is thrown?
>
> Regards,
> Bernd
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
(Continue reading)

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xianran li | 4 Sep 04:11
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question about Bio::DB::GFF


  Hi,

  I tried to load the  gff3 file with load_gff.pl and extrac some information with Bio::DB::GFF. Althougth
this code work properly under windows xp, the $seg got nothing when i run it under Linux. 

  Here is my code and the gff3 file,
  ####################################################################

    #!/usr/local/bin/perl -w

  use strict;
use Bio::SeqIO;
use Bio::DB::GFF; 

  my $in_gff = Bio::DB::GFF->new( -adaptor    => 'dbi::mysqlopt',
                                -dsn        => 'dbi:mysql:test',
                                -aggregator => ['coding'],
                                -user       => "lixr",
                                -pass       => "123456"
                                );                           
my $seg = $in_gff->segment'BGIOSIBCE000001.1');
print $seg->abs_start."\n"; 

  ##################################################################
  ##gff-version 3 
##sequence-region       Chr01   1       43037
Chr01 bgf mRNA 18113 20165 . + . ID=BGIOSIBCE000001.1
Chr01 bgf CDS 18113 19150 . + 0 Parent=BGIOSIBCE000001.1
Chr01 bgf CDS 19344 20165 . + 0 Parent=BGIOSIBCE000001.1
(Continue reading)

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Chris Fields | 4 Sep 06:04
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Re: question about Bio::DB::GFF

Not sure if the gff3 you show was modified for demonstration here but  
it should always be tab-delimited.  Also, I have had problems myself  
when using files with Windows/Mac Classic line endings on UNIX'y  
systems (Excel and a few other Mac OS X programs insist on adding \r  
instead of \n, which plays havoc with parsers sometimes even with  
readline fixes).

chris

On Sep 3, 2007, at 9:11 PM, xianran li wrote:

>
>   Hi,
>
>   I tried to load the  gff3 file with load_gff.pl and extrac some  
> information with Bio::DB::GFF. Althougth this code work properly  
> under windows xp, the $seg got nothing when i run it under Linux.
>
>   Here is my code and the gff3 file,
>   ####################################################################
>
>     #!/usr/local/bin/perl -w
>
>   use strict;
> use Bio::SeqIO;
> use Bio::DB::GFF;
>
>   my $in_gff = Bio::DB::GFF->new( -adaptor    => 'dbi::mysqlopt',
>                                 -dsn        => 'dbi:mysql:test',
>                                 -aggregator => ['coding'],
(Continue reading)

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xianran li | 4 Sep 06:58
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回复： Re: question about Bio::DB::GFF

Hi, everybody,

  It looks like for the different perl version(5.8.8 of  windows and 5.8.5 for linux). And I fixed this problem
by adding ";Name=XXXX" after each line with "mRNA"
  ##############################################################################
  Chr01 bgf mRNA 18113 20165 . + . ID=BGIOSIBCE000001.1;Name=BGIOSIBCE000001.1
Chr01 bgf CDS 18113 19150 . + 0 Parent=BGIOSIBCE000001.1
    ##############################################################################

  This time my code works properly.

  Xianran

Chris Fields <cjfields <at> uiuc.edu> 写道：
  Not sure if the gff3 you show was modified for demonstration here but 
it should always be tab-delimited. Also, I have had problems myself 
when using files with Windows/Mac Classic line endings on UNIX'y 
systems (Excel and a few other Mac OS X programs insist on adding \r 
instead of \n, which plays havoc with parsers sometimes even with 
readline fixes).

chris

On Sep 3, 2007, at 9:11 PM, xianran li wrote:

>
> Hi,
>
> I tried to load the gff3 file with load_gff.pl and extrac some 
> information with Bio::DB::GFF. Althougth this code work properly
(Continue reading)

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Jay Hannah | 4 Sep 16:31
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Re: display protein/CDS multiple sequence alignments with exon boundaries

On Aug 31, 2007, at 4:29 AM, Albert Vilella wrote:
> Probably a bit of a long shot but does anyone have code for
> displaying protein or CDS multiple sequence alignments with the exon
> boundaries of each gene in the alignment?
>
> Something in the bioperl world without funky external dependencies.  
> I think
> it would be an awesome addition to the howtos.
>
> Currently, the Bio::Graphics howto has cdna to genome mapping  
> scripts or
> blast output scripts, but
> I couldn't find code for dealing with multiple sequence alignments.

I'm currently under the (potentially uninformed) impression that  
Bio::Graphics and related tools only work with a single  coordinate  
system. I've never seen a multiple sequence alignment example.

(
   I Google'd for "gbrowse alignment" and hit this:
   http://maizeapache.danforthcenter.org/cgi-bin/gbrowse.cgi

   Click the second Example link and you'll see exons mapped out.

   But zooming all the way in with all the tracks turned on it looks  
like the AZM tracks are just the coding regions. I don't see any  
multiple sequence alignment...
)

I doubt that helped.  :)
(Continue reading)

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Chris Fields | 4 Sep 17:28
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Re: display protein/CDS multiple sequence alignments with exon boundaries


On Sep 4, 2007, at 9:31 AM, Jay Hannah wrote:

> On Aug 31, 2007, at 4:29 AM, Albert Vilella wrote:
>> Probably a bit of a long shot but does anyone have code for
>> displaying protein or CDS multiple sequence alignments with the exon
>> boundaries of each gene in the alignment?
>>
>> Something in the bioperl world without funky external dependencies.
>> I think
>> it would be an awesome addition to the howtos.
>>
>> Currently, the Bio::Graphics howto has cdna to genome mapping
>> scripts or
>> blast output scripts, but
>> I couldn't find code for dealing with multiple sequence alignments.
>
> I'm currently under the (potentially uninformed) impression that
> Bio::Graphics and related tools only work with a single  coordinate
> system. I've never seen a multiple sequence alignment example.
>
> (
>    I Google'd for "gbrowse alignment" and hit this:
>    http://maizeapache.danforthcenter.org/cgi-bin/gbrowse.cgi
>
>    Click the second Example link and you'll see exons mapped out.
>
>    But zooming all the way in with all the tracks turned on it looks
> like the AZM tracks are just the coding regions. I don't see any
> multiple sequence alignment...
(Continue reading)

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