[Biojava-l] Problem with blast file parser

Mark Schreiber markjschreiber at gmail.com
Mon Jan 26 02:45:25 UTC 2009

Have you tried parsing the XML output. While the text parser does
'fake' XML by emitting SAX events I think that the XML parser may be a
lot more stable (the XML output of blast is more stable, at least
recently anyway).

I know this isn't the best solution to your problem but the default
text output of BLAST is not the most parseable. In fact it is probably
the least machine readable of all the blast outputs and definitely the
least stable.

- Mark

On Sun, Jan 25, 2009 at 7:54 PM, Charles Imbusch <charles at imbusch.net> wrote:
> Hello Mark,
> same here. I'm parsing plain text output.
> Cheers,
>  Charles
> Mark Schreiber schrieb:
>> Is this XML parsing or blast text output?
>> - Mark

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