[Biojava-l] Problem with blast file parser

Mark Schreiber markjschreiber at gmail.com
Tue Jan 27 00:55:32 UTC 2009

You can generate plain text from XML using an XSLT. It probably won't
be identical to the BLAST text output but that format is not so stable

On Mon, Jan 26, 2009 at 7:04 PM, Charles Imbusch <charles at imbusch.net> wrote:
> Hello Mark,
> no I haven't tried to parse XML output from Blast.
> Just because of the fact that plain text output can be
> viewed with any editor. That's still very convenient.
> But I'm keen: is there actually an easy to use program for viewing
> XML output?
> Another option would be to generate XML and plain text
> output from Blast at the same time (in one run). But I couldn't find a
> way to do so. Maybe I missed something?
> Cheers,
>  Charles
> Mark Schreiber schrieb:
>> 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

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