[ensembl-dev] Problem with DumpAlignedGenes.pl script

[Harris, Ronald Alan]

Hi Kathryn and Stephen,

Thanks for helping me out with DumpAlignedGenes.pl. The scripts that both of you sent me now work, but there is another problem. According to the help, you can get alignments from multiple species using this:

[--set_of_species species1:species2:species3:...]

I ran both of your scripts with this command line

perl DumpAlignedGenes.pl --set_of_species "human:rat:mouse"

but I get this error (line numbers based on the script Kathryn sent):

-------------------- WARNING ----------------------
MSG: No Bio::EnsEMBL::Compara::MethodLinkSpeciesSet found for
  <EPO_LOW_COVERAGE> and homo_sapiens(GRCh37), rattus_norvegicus(RGSC3.4), mus_musculus(NCBIM37)
FILE: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm LINE: 508
CALLED BY: DumpAlignedGenes.kathryn.pl  LINE: 385
Ensembl API version = 67
---------------------------------------------------
-------------------- EXCEPTION --------------------
MSG: The database do not contain any EPO_LOW_COVERAGE data for human:rat:mouse!
STACK toplevel DumpAlignedGenes.kathryn.pl:389
Ensembl API version = 67
---------------------------------------------------

This is after setting the alignment_type to "EPO_LOW_COVERAGE" which is what I want to use, but I get a similar error if I use the default alignment_type of BLASTZ_NET.

What I ultimately want to do is pull out multiple alignments for all species in the 35 eutherian mammals EPO_LOW_COVERAGE for a set of genes that I am interested in analyzing. Can I do that with this script?

Thanks,

Alan


________________________________
From: dev-bounces at ensembl.org [dev-bounces at ensembl.org] On Behalf Of Kathryn Beal [kbeal at ebi.ac.uk]
Sent: Thursday, May 31, 2012 5:24 AM
To: Ensembl developers list
Subject: Re: [ensembl-dev] Problem with DumpAlignedGenes.pl script

Hi Alan,
As you may have noticed, this script has not been updated for some time. I've made various updates and the script now works. I've committed this to the cvs ensembl-compara HEAD code. I'll send a separate email with this attached for you.

Cheers
Kathryn

Hi,

I am trying to use the DumpAlignedGenes.pl in version 67 of the ensembl-compara API. I have made the following necessary changes to the script (attached script has these changes):

1. When running the script without arguments as a test I get this error:

------------------ DEPRECATED ---------------------
Deprecated method call in file DumpAlignedGenes.pl line 365.
Method Bio::EnsEMBL::DBSQL::MetaContainer::get_Species is deprecated.
Call is deprecated. Use $self->get_common_name() / $self->get_classification() / $self->get_scientific_name() instead
Ensembl API version = 67
---------------------------------------------------
-------------------- EXCEPTION --------------------
MSG: No matches found for name 'Homininae Homo sapiens' and assembly '--undef--'
STACK Bio::EnsEMBL::Compara::DBSQL::GenomeDBAdaptor::fetch_by_name_assembly /home/rharris1/work/ensembl/api/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm:131
STACK toplevel DumpAlignedGenes.pl:369
Ensembl API version = 67

I changed line 365 from

my $this_binomial_id = $this_meta_container_adaptor->get_Species->binomial;

to

my $this_binomial_id = $this_meta_container_adaptor->get_scientific_name;
$this_binomial_id =~ s/\s/_/;

which fixes this error.

2. I also get this similar error:

------------------ DEPRECATED ---------------------
Deprecated method call in file DumpAlignedGenes.pl line 436.
Method Bio::EnsEMBL::DBSQL::MetaContainer::get_Species is deprecated.
Call is deprecated. Use $self->get_common_name() / $self->get_classification() / $self->get_scientific_name() instead
Ensembl API version = 67
---------------------------------------------------
-------------------- EXCEPTION --------------------
MSG: No matches found for name 'Murinae Rattus norvegicus' and assembly '--undef--'
STACK Bio::EnsEMBL::Compara::DBSQL::GenomeDBAdaptor::fetch_by_name_assembly /home/rharris1/work/ensembl/api/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm:131
STACK toplevel DumpAlignedGenes.pl:440
Ensembl API version = 67
---------------------------------------------------

I changed line 436 from

my $source_binomial_id = $meta_container_adaptor->get_scientific_name;

to

my $source_binomial_id = $meta_container_adaptor->get_scientific_name;
$source_binomial_id =~ s/\s/_/;

which fixes this error.

---------------------------------------------------------------------

Now I am getting this error:

Can't call method "get_all_Genes" on unblessed reference at DumpAlignedGenes.pl line 463.

Here is line 463:

my $mapped_genes = $align_slice->{'slices'}->{$source_genome_db->name}->get_all_Genes(

>>>How do I fix this error?<<<


Thank you for your time.

Alan


R. Alan Harris, Ph.D.
Assistant Professor
Bioinformatics Research Laboratory
Epigenomics Data Analysis and Coordination Center
Department of Molecular and Human Genetics
Baylor College of Medicine
Houston, TX 77030
713-798-7695
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