[Bioperl-l] quotes in features

[Brian Osborne]

Mike,

I don't know which databases you're referring to but with the DBD::mysql and
DBD::Oracle drivers you can do things like this:

$gene = $dbh->quote($gene)

And then insert, no problem. This handles all embedded quotes that I've come
across. Forgive me if this doesn't address the issues you have in mind. Yes,
parsing is another story...

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Michael Muratet
Sent: Thursday, July 17, 2003 2:00 PM
To: info at ncbi.nlm.nih.gov
Cc: bioperl-l at bioperl.org
Subject: [Bioperl-l] quotes in features

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..

Thank you.

Mike
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