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

[Elia Stupka]

> DBD::mysql::st execute failed: You have an error in your SQL syntax near
> ')' at line 1 at

Dear Raphael,

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?

> This indicates to me that LOCUS record is getting parsed with something
> like:
> split(/\s+/, $ln); 
> rather than using 
> substr($ln, ??, ??); 

This one is actually down to the bioperl parser, will have a look into it,
wonder if the substr will not cause new, different bugs...

Elia

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