[ensembl-dev] Error in dump_transcripts.pl from the blog post Human BodyMap 2.0 data from Illumina

[Jerry Li]

Thank you, Thibaut, for the response.  The script dump_transcripts.pl now
runs after I upgraded my version of perl.

I have some more questions after running the script. Hopefully the Ensembl
community can help me out.

1)  Is it possible to output the gene id as a Entrez Gene_id.  I only get
output for the ensembl gene stable_id by $gene->stable_id.  But this id is
internal to ensembl right?  How I find out the public gene id or gene name
based on the stable_id?

2)  Is there a way to get the counts or the number of mRNAs that map to
a particular Exon or Transcript?

Thank you all in advance!

Jerry


On Fri, Aug 24, 2012 at 7:15 AM, th3 <th3 at sanger.ac.uk> wrote:

> Hi Jerry,
> You need bioperl in your PERL5LIB.
> We are using bioperl-1.2.3 so I would recommend you to use this one. (But
> the newest bioperl should work too)
>
> Hope this help
>
> Thibaut
>
> ==============================**==============================**==
>
> I ran the script dump_transcripts.pl listed above and got a whole bunch
> of errors such as those listed below. Does the new release of Ensembl 68
> have something to do with it where modules were changed? I re-installed
> Emsembl API but it still doesn’t work. Perhaps the name of the modules
> changed thus they need to be changed in the script as well? Please advice.
> Thank you!
>
> Error Output:
> ——————– WARNING ———————-
> MSG: ‘Bio::EnsEMBL::DBSQL::**GeneAdaptor’ cannot be found.
> Exception Can’t locate Bio/PrimarySeqI.pm in @INC (
>
> BEGIN failed–compilation aborted at /home/jli/src/ensembl/modules/**Bio/EnsEMBL/Slice.pm
> line 62.
> Compilation failed in require at /home/jli/src/ensembl/modules/**
> Bio/EnsEMBL/DBSQL/**SliceAdaptor.pm line 99.
> BEGIN failed–compilation aborted at /home/jli/src/ensembl/modules/**
> Bio/EnsEMBL/DBSQL/**SliceAdaptor.pm line 99.
> Compilation failed in require at /home/jli/src/ensembl/modules/**
> Bio/EnsEMBL/DBSQL/GeneAdaptor.**pm line 67.
> BEGIN failed–compilation aborted at /home/jli/src/ensembl/modules/**
> Bio/EnsEMBL/DBSQL/GeneAdaptor.**pm line 67.
> Compilation failed in require at (eval 8) line 3.
>
> FILE: Bio/EnsEMBL/Registry.pm LINE: 1015
> CALLED BY: dump_transcripts.pl LINE: 88
> Date (localtime) = Thu Aug 23 16:54:56 2012
> Ensembl API version = 68
>
> Jerry
>
>
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