[ensembl-dev] trying to get homology gene sequence

[Feifei Zhang]

Hello Ensemble team,

I was trying to get DNA sequences from a list of orthologous genes among a
group of species by using the Compara API. The API version used is 69 in
windows 7.

I started by following the answer to one of the FAQs, which I thought was
quite similar to my question: 'How do I get alignments of homologous
proteins? Can I get the CDS (coding sequence) alignments as well? I'm using
the API'. 'Yes, both can be obtained using the Compara API: see this example
script<http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-compara/scripts/examples/tree_printAlignment.pl?revision=1.2&root=ensembl&view=markup>'.
Thus, I downloaded the code 'tree_printAlignment.pl' and tried to run it in
my laptop by typing 'perl tree_printAlignment.pl' under the directory
'C:\src'. If it works, I may try to made some change to get homologies for
the other genes. However, I could not get the 'example script' work in my
computer. The error massage it gave is: MSG:
'Bio::EnsEMBL::Compara::DBSQL::GeneTreeAdaptor' cannot be found.

To give you some info of how I installed API and set up environment, here
is what I did. First I installed Perl and DBD::MySQL package. I created an
installation directory named 'src' under C, then I downloaded API packages
including 'ensembl', 'ensembl-compara', 'ensembl-variation',
'ensembl-functgenomics', and 'BioPerl 1.2.3' into folder 'src'. Then, I set
up my environment. Since I am using windows, I typed 'set
PERL5LIB=C:\src\bioperl-1.2.3;C:\src\ensembl\modules;C:\src\ensembl-compara\modules'
into the command prompt. Then I went to the page '
http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-compara/scripts/examples/tree_printAlignment.pl?view=annotate&root=ensembl'
and downloaded the code as 'tree_printAlignment.pl' and tried to run it. I
am a little suspicious about my environment setting. But I do not know what
the problem is. I appreciate if someone can help me out with this.


Best,

Feifei
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