[Bioperl-l] bad entries in interpro

Hilmar Lapp hlapp at gmx.net
Sat Nov 27 01:03:05 EST 2004

On Friday, November 26, 2004, at 06:58  PM, Allen Day wrote:

> the problem is that iprscan (the program that produces the interpro xml
> files) does not properly xml-escape some characters.  there is an 
> if-block
> in the module that tries to catch things like quotes and ampersands, 
> but
> it's by no means exhaustive.

I looked at the module and now I'm confused. Did I miss something or 
can you explain why

   my $zinc = "(\"zincins\")";
   my $wing = "\"Winged helix\"";
   my $finger = "\"zinc finger\"";

had to be hard-coded? I would have thought you wanted to encode (and 
catch!) the quotes, not the phrase Winged helix?

Also, did you check whether CGI.pm or a LWP module or some such doesn't 
solve this problem generically enough?

Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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