[BioPython] Syntax error while parsing Blast output

Peter biopython at maubp.freeserve.co.uk
Wed Oct 24 08:22:45 UTC 2007


[Sorry you got this twice Michiel, I forgot to set the from/to fields]

> That part of the tutorial is in the section "Deprecated BLAST parsers", which
> will be removed once the plain-text Blast parser is removed from Biopython.
> ...
> Nevertheless, it may be a good idea to remove the plain text Blast parser
> completely from Biopython in the upcoming release (which will probably be
> done this week), to avoid further confusion.

Removing it sounds too drastic - especially as we have had people on
the mailing list using it  deliberately fairly recently.  If you really do want
to remove this code, then adding a deprecation warning to the plain text
parser for the next release would be a more gentle route.

I think there is still some benefit in having the plain text parser, and that
it could be fixed to cope with current multi-query files without too much
pain.  Maybe I should try this weekend...

Anyone want to voice their opinion?

Peter



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