[Bioperl-l] Trying to get a mysql DB from genbank flat files

[Elia Stupka]

> quote 
> $sql = $dbh->quote($string); 
> This method escapes special characters (quotation marks, etc.) from strings
> and adds the required outer quotation marks. May not be able to handle all
> types of input (i.e binary data). 

Excellent, thank you guys for all the suggestions!

Elia


> 
> Example using the above methods: 
> #!/usr/bin/perl -w 
> use DBI; 
> use strict; 
> my $dbh = DBI->connect("DBI:mysql:contacts",undef,undef) 
> or die "Unable to connect to contacts Database: $dbh->errstr\n"; 
> my $sth = $dbh->prepare("SELECT uid FROM contact WHERE last_name =
> 'Flaherty'"); 
> $sth->execute or die "Unable to execute query: $dbh->errstr\n"; 
> my $row = $sth->fetchrow_arrayref; 
> my $uid = $row->[0]; 
> $sth->finish; 
> my $newname = $dbh->quote("The Flahertys'"); 
> my $statement =qq(UPDATE contact SET last_name = '$newname' 
>                   WHERE uid = $uid); 
> my $rc = $dbh->do($statement) or die "Unable to prepare/execute $statement:
> $dbh->errstr\n"; 
> print "$rc rows were updated\n"; 
> $dbh->disconnect; 
> exit; 
> 
> Brian O.
> 
>  -----Original Message-----
> From: 	Wilfred Li, Ph.D. [mailto:wilfred@sdsc.edu] 
> Sent:	Thursday, November 15, 2001 12:41 PM
> To:	bioperl-l@bioperl.org
> Subject:	RE: [Bioperl-l] Trying to get a mysql DB from genbank flat
> files
> 
> >thanks for your mail, you have magically bumped into our daily nightmare,
> >that is that very often people put crazy characters in the description
> >lines, and we have to find ways of backslashing all of them otherwise
> >they will break mysql statements. Could you mail me the offending record?
> Hi,
> 
> If bind variables are used in place of a plain insert statement, many of
> the special characters will be taken care of by perl DBI. e.g.
> 
> $sth->prepare("insert ... values (?, ..., ?)");
> $sth->execute($id, ..., $kw);
> 
> or use
> 
> $dbh->do("insert ... values (?, ..., ?)", $id, ..., $kw);
> 
> to combine the two steps into one.
> 
> I had the problem with SeqAdaptor.pm when parsing SwissProt.
> 
> Wilfred
> 
> 
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