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Troubles with '<' in PROSITE

Guy Bottu gbottu at bigben.vub.ac.be
Wed Sep 16 05:48:40 EST 1998

from : the Belgian EMBnet Node

        Dear fellow SRS server managers,

I discovered another problem with the parsing of PROSITE entries. Some
PROSITE patterns start with a '<'. Netscape takes this for the begin of
a "tag" and so part of the entry gets messed up. Take e.g. a look at the
entry [prosite-id:TONB_DEPENDENT_REC_1]. The cure :

in prosite.is add :

hl_patt: ~ {$In:[fields c:patt t:html]}
           'PA' '<'? {$Rep:'&lt;'} ~

In PROSITEDOC there are some more '<' characters that cause trouble, see
e.g. [prositedoc-id:PDOC00535] where the <Ca> gets lost. Again, the cure :

in prositedoc.is replace :

h_des:   ~ {$In:[fields c:des t:html]}
           (/PDOC[0-9]+/ {$Rep:{$parStr:prositedocR $Ct $Ct}} |
           /(EC +)([0-9]\\.[0-9.]+)/{$Rep:{"$1($parStr:enzymeR)" $2 $2}} |
           /[a-zA-Z0-9]+/ | /[^a-zA-Z0-9]+/
           )* ~

by :

h_des:   ~ {$In:[fields c:des t:html]}
           (/PDOC[0-9]+/ {$Rep:{$parStr:prositedocR $Ct $Ct}} |
           '<' {$Rep:'&lt;'} |
           /(EC +)([0-9]\\.[0-9]+\\.[0-9]+\\.[0-9]+)/
            {$Rep:{"$1($parStr:enzymeR)" $2 $2}} |
           /[a-zA-Z0-9]+/ | /[^a-zA-Z0-9<]+/
           )* ~

        Dr. Guy Bottu

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