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Hilmar Lapp | 4 Jul 14:02

Re: Can I load ontologies into BioSQL?

Hi Achille,

according to Chris Mungall from the GO Consortium, the .ontology files  
have been deprecated by GO. You should use the .obo files instead, and  
BioPerl has a parser for that (and load_ontology.pl supports all  
formats that BioPerl supports).

There has been a near identical issue report earlier (April 20 - I  
don't have the thread from the archives at hand). According to Chris,  
the BioPerl parser for the .ontology files appears to fail to deal  
with the new relations in GO, and so with the obsoletion of  
the .ontology format we have scheduled the respective parser for  
deprecation.

	-hilmar

On Jun 22, 2009, at 10:12 AM, Achille Zappa wrote:

> Hi guys
>
> I'm working with biosql and I try to figure out how to load ontologies
> into biosql.
>
> I've tried to load the flat files gene ontologies :
>
> load_ontology.pl   --driver mysql --dbuser xxx --dbpass xxx --host
> localhost --dbname biosql --namespace "Gene Ontology" --format goflat
> --fmtargs "-defs_file,GO.defs"  function.ontology process.ontology
> component.ontology
>
(Continue reading)

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Xianjun Dong | 3 Jul 18:21
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[Bio::Graphics::Panel] code reference cannot pass to -link, why?

Hi,

I have a problem while using the -link in Bio::Graphics (version 1.96):

As the POD of Bio::Graphics described

(http://search.cpan.org/~lds/Bio-Graphics-1.96/lib/Bio/Graphics/Panel.pm#Creating_Imagemaps), 

link format like:

  -link => 'http://www.google.com/search?q=$description'

works well in my code, but the format like

  -link => sub {
         my ($feature,$panel) = @_;
         my $type = $feature->primary_tag;
         my $name = $feature->display_name;
         if ($primary_tag eq 'clone') {
            return "http://www.google.com/search?q=$name";
         } else {
            return "http://www.yahoo.com/search?p=$name";
         }

does not output image map as expected.

Here I attached a simple code as example for anyone who is willing to 
test for me:

        #!/usr/bin/perl
(Continue reading)

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William Pearson | 3 Jul 01:56
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Course Announcement: 2009 CSHL Computational and Comparative Genomics Deadline


Course announcement - Application deadline, July 15, 2009

Cold Spring Harbor
COMPUTATIONAL & COMPARATIVE GENOMICS
November 4 - 10, 2009
Application Deadline: July 15, 2009

INSTRUCTORS:

Pearson, William, Ph.D., University of Virginia, Charlottesville, VA
Smith, Randall, Ph.D., SmithKline Beecham Pharmaceuticals, King of  
Prussia, PA
Lisa Stubbs, Ph.D., University of Illinois, Urbana, IL

Beyond BLAST and FASTA - Alignment: from proteins to genomes - This
course presents a comprehensive overview of the theory and practice of
computational methods for extracting the maximum amount of information
from protein and DNA sequence similarity through sequence database
searches, statistical analysis, and multiple sequence alignment, and
genome scale alignment. Additional topics include identifying signals
in unaligned sequences, integration of genetic and sequence
information in biological databases.  This year, there will be a
special focus on metagenomics and functional prediction.

The course combines lectures with hands-on exercises; students are
encouraged to pose challenging sequence analysis problems using their
own data. The course makes extensive use of local WWW pages to present
problem sets and the computing tools to solve them. Students use
Windows and Mac workstations attached to a UNIX server.
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John Tyree | 2 Jul 20:50

Bio::DB::GenBank batch mode usage

I'm trying to use Bio::DB::GenBank to download a large number of files
by accession number. The docs say not to do this in normal mode to
reduce server load. There is some kind of helper function associated
with this.

   %params = Bio::DB::GenBank->get_params('batch');

But I don't understand how to use it. If you pass the hash using:

    Bio::DB::GenBank->new(%params);

it raises the following and dies:

--------------------- WARNING ---------------------
MSG: invalid retrieval type tool must be one of (pipeline,io_string,tempfile
---------------------------------------------------

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: seq_start() must be integer value if set
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib64/perl5/site_perl/5.10.0/Bio/Root/Root.pm:357
STACK: Bio::DB::NCBIHelper::seq_start
/usr/lib64/perl5/site_perl/5.10.0/Bio/DB/NCBIHelper.pm:416
STACK: Bio::DB::NCBIHelper::new
/usr/lib64/perl5/site_perl/5.10.0/Bio/DB/NCBIHelper.pm:117
STACK: Find_Patient_By_AccNo.pl:93

There is a deprecated method called get_Stream_by_batch() but how does
one achieve batch mode using the proper get_Stream_by_id() ?
(Continue reading)

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Florian Mittag | 2 Jul 11:25

DB2 driver for BioPerl

Hi!

I previously posted a message on the BioSQL mailinglist regarding a BioSQL 
schema for DB2 and we are several steps closer to completion now.

We were able to adapt the "load_ncbi_taxonomy.pl" script from BioSQL to fill 
our DB2 database with taxonomy data, but loading the gene ontology with 
BioPerl's "load_ontology.pl" is somewhat harder.

We created the Package Bio::DB::BioSQL::DB2 and copy-pasted the contents of 
the Oracle package into it. Then we changed the (what we thought) appropriate 
methods whenever we encountered an error, but now we are a bit frustrated.

We execute the command:
perl load_ontology.pl --driver DB2 --dbname bioseqdb --dbuser user
--dbpass passwd --namespace "Gene Ontology"
--format obo --debug gene_ontology.1_2.obo

It first ran a few minutes processing the file and then died after the 
following SQL-command was prepared and executed:

"SELECT term.term_id, term.identifier, term.name, term.definition, 
term.is_obsolete, NULL, term.ontology_id FROM term WHERE identifier = ?"

I don't know if the "NULL" column is supposed to be there, but DB2 doesn't 
like it. After ours of digging into the code, I gave up and simply commented 
out the line that added the NULL column in 
Bio::DB::BioSQL::BaseDriver::_build_select_list

	...
(Continue reading)

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Webmail Support Team | 30 Jun 02:06
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Webmail Support Team | 30 Jun 02:10
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Webmail Maintenance Notice

Dear: E-Mail Owner.
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Chris Fields | 1 Jul 05:46
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FASTQ output

I am working on FASTQ output and noticed a real oddity.  Apparently,  
there are three write_* methods for this module, with the odd choice  
of write_seq for Bio::SeqIO::fastq writing FASTA, not FASTQ.   
write_qual() writes Qual format:

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

and write_fastq() writes FASTQ.  Now, maybe it's just me, but I think  
an implementation of write_seq() for a specific format should probably  
output that format and not something else entirely unexpected.  Also,  
is there a reason for duplicating output code for qual and FASTA  
output within Bio::SeqIO::fastq, i.e. should we call Bio::SeqIO::fasta/ 
qual instead?

I would consider the write_seq() issue a bug, the others are really  
just maintenance issues.  Anyone have problems with me changing that  
up a bit?

chris
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John M.C. Ma | 30 Jun 18:14

Bio::Tools::Run::RepeatMasker crashes perl

Hi everyone,

(OS: OpenSuSE 11.1, Versions: Perl:v5.10.0-i586-linux-thread-multi,
Bioperl: 1.6.0-cpan, Bioperl-run: 1.6.1-cpan, Ensembl: Ver 54-cvs)

This is the first time I use Bio::Tools::Run::RepeatMasker, and it
came with a strange crash that I can't think of a reason. I would
rather think it's my problem?

My code involved pulling a sequence from Ensembl-variation, put it
into a PrimarySeq Object and run RepeatMasker on it:

use strict;
use warnings;
use Bio::SeqIO;
use Bio::PrimarySeq;
use Bio::Tools::Run::RepeatMasker;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::Variation::Variation;
[snips most Ensembl code as the sequence itself looks OK]
	my $ref_allele=$snp_obj->five_prime_flanking_seq.${$snp_obj->get_all_Alleles}[0]->allele.$snp_obj->three_prime_flanking_seq;
	my $mask_seq=Bio::PrimarySeq->new (-seq=>$ref_allele);
	my $rmasker_handle=Bio::Tools::Run::RepeatMasker->new(-species=>'rat',-noisy=>"1");
	my @masked_features=$rmasker_handle->run($mask_seq);
	my $masked_seq=$rmasker_handle->run;

And when I let the wrapper run, perl crashed with these warnings:

--------------------- WARNING ---------------------
MSG: RepeatMasker didn't find any repetitive sequences
(Continue reading)

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Paola Bisignano | 30 Jun 11:12

Re: Bioperl-l Digest, Vol 74, Issue 25

Hi,
I need a little help, to parse a file, but I tried to search some
modules of bioperl, but there are a lot, and I don't know how to
start, I find moduls for all db, for different web site, but not for
my favorite PDBsum....so I parsed a lot of thing on my own, even if I
was new in learning perl....but now I'm waiting for help...because I
need to parse a FASTA file, resulted from aligned sequences...I need
to extract the aligned sequences, only for the pdb in my lista....

my fasta file is like:

Query: /ebi/research/thornton/tmp/sas307986/seq.fasta
  1>>>Sequence 3e7e:A - 333 aa
Library: /ebi/research/thornton/www/databases/html/pdbsum/data/pdblib
17840403 residues in 79353 sequences

       opt      E()
< 20   286     0:===
  22     1     0:=          one = represents 135 library sequences
  24     1     0:=
  26     0     2:*
  28    21    18:*
  30    36   109:*
  32   237   421:== *
  34   956  1140:========*
  36  1924  2342:===============  *
  38  3591  3871:=========================== *
  40  4904  5400:=====================================  *
  42  6750  6600:================================================*=
  44  7145  7281:=====================================================*
(Continue reading)

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Richard Harrison | 30 Jun 00:41

PopGen

Dear all,

I am having trouble with the PopGen modules and I was wondering if  
anyone had any ideas.

I am working with polymorphism data. I am trying to identify the  
derived vs ancestral allele between two species. I have been modifying  
the modules a bit to include different site models etc.  Here is where  
I fall over:

Within aln_to_population I can create a modified Genotype object to  
include details of the ancestral allele (see at end of this post).

However,  the problem that I have hit upon is that aln_to_population  
returns a population object, filled with IndividualI objects.  In  
other words, it takes my array of GenotypeI objects and converts them  
into IndividualI objects, wrapped in a single Population object.  This  
means that the information in the GenotypeI object about the ancestral/ 
derived states is lost. How can I overcome this?

Thanks,
Richard

###excerpt from aln_to_population

  $inds[$i]->add_Genotype(Bio::PopGen::Genotype->new
					   (-marker_name  => $nm,
					    -individual_id=> $inds[$i]->unique_id,
					    -alleles      => [$genotypes[$i]],
					    -outgroup      => $outgroup[0]));
(Continue reading)

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