[Bioperl-l] quotes in features

[Ewan Birney]

On Thu, 17 Jul 2003, Michael Muratet wrote:

> Greetings
>
> I found the following entry in gbpri1.seq.gz
>
> LOCUS       AB078028                 510 bp    mRNA    linear   PRI
> 17-JUL-2002
> DEFINITION  Homo sapiens ATF3deltaZip2exonD'DE'E gene for ATF3deltaZip2,
>             partial cds.
>                      /gene="ATF3deltaZip2exonD'DE'E"
>      CDS             <1..60
>                      /gene="ATF3deltaZip2exonD'DE'E"
>                      /codon_start=1
>
> Embedded quotes are a problem for us who try to automatically parse
> and/or store in databases the information in the DEFINITION or CDS or
> /gene fields. We can deal with them, but adding code for special cases
> (and figuring out what those cases are) is time consuming. I'd like to
> propose a standard that says that strings that represent names, genes,
> etc., contain no spaces, quotes, or non-printing characters, or anything
> else that might be construed as a delimiter in perl, C, Java, SQL, etc..
>

Mike - this is a good point, but the Feature table has very long
established rules about quoting etc and we are not going to be changing
those. If the Bioperl parser falls over on these guys, then this is a
bioperl error which we should fix.


there is simply no sense (or pragmatic way) to change the feature table
parsing rules.



> Thank you.
>
> Mike
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