[Bioperl-l] Entrez Gene ASN parsers
Mingyi.Liu at gpc-biotech.com
Sun Mar 13 00:17:59 EST 2005
> > My parser does to NCBI's ASN.1 EntrezGene file what an XML
> parser does
> > to a yet-to-exist XML-formatted EntrezGene file (or better
> than it, if
> > NCBI decides to code Entrez Gene in the XML format that Eutils
> > provide).
> This is apparently what they will be doing, or at least my
> understanding of it.
That's logical, but not good. I really don't like the XML format Eutils provided. In fact, I heard few people did.
> The question is how safe are your regexps from possibly unexpected
> things like escaped quotes or an escaped curly brace that's part of a
> string and not end of an entity etc or whatever might confuse your
It's not a problem. In my parsers these situations are dealt with already. So far, nothing in the latest human, mouse, rat breaks the parser. I didn't test on other genomes, but they should work fine.
BTW, an unrelated question: Do you know why is it that my reply mails always started new threads in Bioperl-l mailing list archive, whereas others' (like yours) form a nice thread?
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