[BioRuby] newick gsub(' ','_')

Ben Woodcroft donttrustben at gmail.com
Tue Jul 21 01:19:21 UTC 2009


2009/7/20 Naohisa Goto <ngoto at gen-info.osaka-u.ac.jp>

> I believe the behavior is right, although I know some software
> ignore the underscore rule.  When parsing Newick format, giving
> :parser => :naive option to Bio::Newick.new() can prevent any
> label character conversion, but no option for the output, because
> I think genarating broken format is generally a bad thing.

OK, thanks - that makes sense. The particular program I'm using, figtree,
understands underscores as spaces, and so I never really had any problem in
the first place.

But to be academic I don't actually agree that the specification says blanks
should be converted underscores in otherwise unquoted strings - I think
quoting them is equally valid (and possibly supported by more programs), but
maybe that's just me. Happy to accept the community judgement on that one.

Would it make sense to allow quoting to be forced by the user? I don't see
anything in the specification that is against that, so long as everything
inside is properly escaped.


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