parse_evidence.ber_pre using BERUniprot

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parse_evidence.ber_pre using BERUniprot

Aaron Buechlein
Hi Everyone,
I'm having some difficulties with the parse_evidence component.  When we
run the component using --evidence_type=BERUniprot, the output file is
always empty.  I've run the uniprot_idmapping_to_mldbm.pl script
thinking this would create the necessary char_db needed for
parse_evidence to assign annotation.  However, this file doesn't appear
to have the appropriate structure needed for
EvidenceParser/BERUniprotParser.pm.  Can someone point me to the
appropriate file or explain how to create the appropriate char_db?
Thanks,

Aaron Buechlein

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Re: parse_evidence.ber_pre using BERUniprot

Joshua Orvis
I'll let him respond here, but I believe Kevin is in the process of writing up a summary of all datafiles needed by the prokaryotic annotation pipeline and (possibly) including a place where they can be downloaded.

Joshua



On Mon, May 23, 2011 at 2:38 PM, Aaron Buechlein <[hidden email]> wrote:
Hi Everyone,
I'm having some difficulties with the parse_evidence component.  When we
run the component using --evidence_type=BERUniprot, the output file is
always empty.  I've run the uniprot_idmapping_to_mldbm.pl script
thinking this would create the necessary char_db needed for
parse_evidence to assign annotation.  However, this file doesn't appear
to have the appropriate structure needed for
EvidenceParser/BERUniprotParser.pm.  Can someone point me to the
appropriate file or explain how to create the appropriate char_db?
Thanks,

Aaron Buechlein

------------------------------------------------------------------------------
What Every C/C++ and Fortran developer Should Know!
Read this article and learn how Intel has extended the reach of its
next-generation tools to help Windows* and Linux* C/C++ and Fortran
developers boost performance applications - including clusters.
http://p.sf.net/sfu/intel-dev2devmay
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users


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