What about the other reserved characters in XML that are valid in FASTA?
"
'
&
Not escaping could also break downstream software - especially with &
which should always begin an escape sequence. :(
-Matt
Brian Pratt wrote:
> Granted, this is a defect - but that's still an unfortunate choice of
> characters. Even with the correction I can imagine this tripping
> up other software downstream since the properly escaped XML would no
> longer match the FASTA on a literal basis. I don't suppose your
> users could be induced to use { and } or [ and ] or ( and ) instead of
> < and > ?
>
> Brian
>
> On Tue, Nov 10, 2009 at 9:43 PM, Simon Michnowicz
> <[email protected] <mailto:[email protected]>> wrote:
>
> Dear Group,
>
> I would like to flag a possible bug in a TPP tool.(Sorry in
> advance if this is the wrong forum to report bugs).
>
> One of our users has reported issues with a tpp pepXML tool (he
> was using Mascot so I assume he was using Mascot2XML.exe).
>
> Our FASTA database has protein entries with special characters in
> then, i.e.
>
> *IFN-<alpha>2*
>
> *&*
>
> *V<beta>14 *
>
> This generated a pepXML file that was not valid xml, as the tags
> were not escaped properly.
>
>
>
>
> *<alternative_protein protein="tr|Q9UMA4|IFN-<alpha>2"
> num_tol_term="2" peptide_prev_aa="-" peptide_next_aa="S"/>*
>
>
>
>
> regards
>
>
>
>
> Simon Michnowicz
> Duty Programmer
> Australian Proteomics Computation Facility
> Ludwig Institute For Cancer Research
> Royal Melbourne Hospital,
> Victoria
> Tel: (+61 3) 9341 3155
> Fax: (+61 3) 9341 3104
>
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