Dealing with results from web services¶

Internally, prunito uses the wonderful requests package and that provides a sophisticated Response object. To avoid losing the power of that object, prunito provides a wrapper around it, the WSResponse class (where WS stands for web service). Or course, format and content of results returned by calls to web services depend on the service and so there are custom subclasses of WSResponse for various web services.

What does WSResponse (sub)classes do?¶

They provide helper methods. For example, size() returns the number of hits if that particular web service gives that information or it can be quickly determined. as_file_obejct() wraps the result’s text representation in io.StringIO. As many results are sequences-like–we do expect one or more hits for a call after all– special methods for sequences are provided wherever possible to allow iteration or slicing. Obviously, this depends on the service and kind of results.

Any attribute they don’t recognize is passed on to the wrapped Response object. This means that things like the the Response’s attributes can be accessed via as expected: text, url, status. Methods like json() are available, too.

Results from searching UniProtKB¶

In addition to what the parent class has, this one also:

Has a method, release(), for getting the current release. Releases are specified as year_number, e.g. 2017_10.
Has a method, date(), to get the date of the current release. This can be returned as a string or a datetime.datetime obejct.
Allows iterating over results for some formats.

When full UniProtKB text entries are retrieved, they are parsed and the iterator returns the Record object. For tabular data, like list, gff or tab, lines are iterated over.
Tabular data can also be returned as a pandas dataframe.

Results from identifiers mappings¶

Results for mapping calls are returned as a table with two columns, From and To. This table can be accessed as text via <obj>.text, the lines can be iterated over but, for convenience, a dictionary of the results is prepared as <obj>.as_dict(). A list of mapped-to target IDs is <obj>.target_ids(). Identifiers that could not be mapped will be silently ignored, i.e., there won’t be any mappings in the result set.

Results from HMMER searches¶

todo See also WSResponseHmmer.

Results from searching EuropePMC¶

todo See also WSResponseEPMC.

Taxonomy results¶

todo See also WSResponseTax.