escaped quotes in newick filenames

[Yan Wong]

Me again! Sorry.

The Bio::Phylo Newick parser doesn't seem to cope with escaped quotes in taxon names. I've attached a test file to demonstrate.

(http://evolution.genetics.washington.edu/phylip/newick_doc.html says: "Single quote characters in a quoted label are represented by two single quotes.")

[Rutger Vos]

Shouldn't they be balanced?

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[Yan Wong]

On Friday, 27 June 2014 22:02:52 UTC+1, Rutger Vos wrote:

Shouldn't they be balanced?

According to the spec (and a number of examples I've found around the internet), doubled-up single quotes don't need to be balanced within names, no. For example, this is a valid taxon used in the Open Tree of Life, which has been newick-validated 

'Planipapillus_sp_''Bennison''s_Lookout''_ott841740':0

[Rutger Vos]

Mmmm.... well, Bio::Phylo doesn't support that :)

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[Yan Wong]

On Monday, 30 June 2014 09:15:04 UTC+1, Rutger Vos wrote:

Mmmm.... well, Bio::Phylo doesn't support that :)

:) Replaced them with standard double quotes for the time being, in case anyone else hits this.