[Biopython-dev] PhyloXML helper functions
chapmanb at 50mail.com
Tue Jul 7 12:51:52 UTC 2009
> I've been mulling a couple of methods for PhyloXML objects that I thought
> could deserve some discussion.
> 1. Singular properties for some plural attributes
> This goes back to the "confidences" issue: When I'm drilling down through a
> phyloXML-derived tree, I keep expecting certain attributes to be singular
> values when they're actually plural. Auto-completion catches it, of course,
> but the resulting code would seem more obvious if I used the singular name
> when I know the attribute consists of a list of one element.
I like the idea and implementation for cases where you can have
multiple items, but have one most of the time. Very nice.
> 2. A find() method on Clade and maybe Phylogeny objects
> - The keyword argument could be a regular expression. Would that be useful?
This seems useful. Often people use crazy naming convention hacks,
and might want to pull out something like all proteins from a
particular organism based on a common prefix in the name.
> To handle numbers, I'd have to convert every sub-node attribute value to a
> string, and that would be weird -- or else find() would have to skip
> numerical attributes.
Is this if you support regular expressions or either way? For the
find, I think it's sufficient to define what you support and leave
it at that set: any subset of searching will help people get their
> - If no regular arguments are needed, cls could default to PhyloElement or
> even "object" to match everything.
I like the object default here. This fits with a simple use case of:
find everything that matches this string of interest.
> - To enable arbitrary hairiness, this function could accept a function as
> the value of the keyword argument and return anything truthy. But at that
> point, the user could probably just roll their own find_node() function.
> However, it could still be useful to filter for numerical values.
This is probably more than you need. For complicated cases I'd
assume people are sophisticated enough to roll their own.
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