EMBOSS and the GenomeReviews databank

[Rodrigo Lopez]

Hi Paul,

Many thanks for the reply. Let's see if Guy has further comments.

R:)


> -----Original Message-----
> From: Paul Kersey [mailto:pkersey at ebi.ac.uk] 
> Sent: 28 July 2004 16:15
> To: rls at ebi.ac.uk
> Cc: 'Guy Bottu'; emboss-dev at embnet.org; genome_reviews at ebi.ac.uk
> Subject: Re: EMBOSS and the GenomeReviews databank
> 
> 
> Rodrigo Lopez wrote:
> 
> >Yes, it is very unfortunate that the genome reviews data is 
> >non-standard. I'm forwarding this to the head of that 
> project. He may 
> >have a comment regarding the evidence tags present/future.
> >
> >R:)
> >
> >
> >  
> >
> >>-----Original Message-----
> >>From: owner-emboss-dev at hgmp.mrc.ac.uk
> >>[mailto:owner-emboss-dev at hgmp.mrc.ac.uk] On Behalf Of Guy Bottu
> >>Sent: 28 July 2004 15:27
> >>To: emboss-dev at embnet.org
> >>Subject: EMBOSS and the GenomeReviews databank
> >>
> >>
> >>	Dear developers,
> >>
> >>I just noticed something that might interest you. At the
> >>EMBL-EBI they 
> >>have a GenomeReviews databank (with complete bacterial 
> chromosomes or 
> >>plasmids in one entry EMBL files). They however decided to 
> >>depart somewhat 
> >>from the EMBL format. When I run 
> >>seqret -feature grv:u00096_gr
> >>I get a lot of error messages of type :
> >>Warning: U00096_GR: Bad value 'AAC77270.1 {EMBL:U00096}' for 
> >>tag '/protein_id'
> >>Warning: bad /protein_id value 'AAC77271.1 {EMBL:U00096}'
> >>
> >>	Sincerely,
> >>	Guy Bottu
> >>
> >>    
> >>
> >
> >  
> >
> Dear Guy
> 
> the evidence tags convey extra information that some users are 
> interested in.  It was not possible to fit this information 
> within the 
> existing definition of EMBL format, hence it was necessary to 
> intorduce 
> the tags.
> 
> However, if you do not want to use the evidence tags, we also 
> distribute 
> a program that removes them from the Genome Reviews files.
> 
> The following comes from the Genome Reviews user manual:
> 
> For users who do not wish to filter information by source, a 
> program is 
> provided with this release to remove evidence tags from 
> Genome Reviews 
> files, resulting in the production of "normal" EMBL format 
> files. This 
> program is written in the Java programming language and will 
> run on any 
> platform on which a Java runtime environment has been installed. Such 
> environments are available free of charge for many platforms 
> (including 
> Microsoft Windows, Mac OS and GNU/Linux) from either Sun Microsystems 
> (URL: http://java.sun.com/j2se/ or your hardware vendor. The 
> tag removal 
> program itself is available:
> 
>     * as source code (RemoveEvidenceTags.jar) from
>       ftp://ftp.ebi.ac.uk/pub/software/genome_reviews/java/uk
>       <ftp://ftp.ebi.ac.uk/pub/software/uk>
>     * as an executable jar file from
>       
> ftp://ftp.ebi.ac.uk/pub/software/genome_reviews/java/RemoveEvi
> denceTags.jar
>       
> <ftp://ftp.ebi.ac.uk/pub/software/genome_reviews/RemoveEvidenc
> eTags.jar>
> 
> 
> Documentation on the use of the tag removal program can be generated 
> after download by one of the following commands (the first command is 
> for use with the RemoveEvidenceTags.java source code; and the second 
> command if for use with the RemoveEvidenceTags.jar file):
> 
>     * javadoc -d destination-directory RemoveEvidenceTags.java
> 
>       (where the destination-directory is the target directory, where
>       you would like the generated documentation to be placed)
> 
>     * jar xf RemoveEvidenceTags.jar
> 
>       (the generated documentation is placed in a directory 
> called javaDoc)
> 
> The procedure to run the tag removal program is also described below:
> 
>    1. Compile the java class, using: javac RemoveEvidenceTags.java
>    2. Run the compiled code using, either:
>       java -cp . uk/ac/ebi/genomeReviews/RemoveEvidenceTags dir
>       or:
>       java -cp . uk/ac/ebi/genomeReviews/RemoveEvidenceTags 
> dir file-name
> 
> 
> Alternatively the program can be run from the executable jar 
> (RemoveEvidenceTags.jar) as follows:
> 
>    1. java -jar RemoveEvidenceTags.jar dir
>       java -jar RemoveEvidenceTags.jar dir file-name
> 
> 
> where dir is the path to the directory where the Genome Reviews files 
> are located, and file-name is the name of a Genome Reviews file 
> contained in this directory. If only the single parameter 
> (file-name) is 
> used, then the program with remove the evidence tags from ALL Genome 
> Reviews files located in that directory. The dir should end with a 
> closing file separator.
> 
> ---
> 
> Best wishes
> 
> Paul
> 
> -- 
> "He could consider civilisation, and see the world as a 
> microcosm of the cell" - Joseph Heller
> 
> ------------------------------------------------------------------
> Dr. Paul Kersey
> EMBL-European Bioinformatics Institute    Tel: +44-(0)1223-494601
> Wellcome Trust Genome Campus, Hinxton     Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK                    email: pkersey at ebi.ac.uk
> 
>