[Biopython-dev] PhyloXML helper functions

[Christian M Zmasek]

Hi:

I cannot really comment on the first point (since I don't know enough 
Python), but I totally agree with Brad on the issue of the find() 
methods -- very useful!

Christian

 
Brad Chapman wrote:
> Hi Eric;
>
>   
>> 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
>>     
> [...]
>   
>> Enhancements:
>> - 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
> work done.
>
>   
>> - 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.
>
> Nice ideas,
> Brad
>