rnaglib.transforms.ResidueAttributeFilter¶

class rnaglib.transforms.ResidueAttributeFilter(attribute, aggregation_mode='min_valid', value_checker=None, min_valid=1, aggfunc=None, **kwargs)[source]¶

Reject RNAs that lack a certain annotation at the whole residue-level.

Parameters:

attribute (str) – Which node-level attribute to look for.
aggregation_mode (str) – str (either “aggfunc” or “min_valid”); if set to “aggfunc”, keeps an RNA if the output of the aggregation function of the residue attribute at the RNA level passes the value_checker; if set to “min_valid”, keeps an RNA if more than min_valid nodes pass the value_checker.
value_checker (Optional[Callable]) – Function that accepts the value of the desired attribute and returns True/False.
aggfunc (Optional[Callable]) – Function to aggregate the residue labels at the RNA level (only if aggregation_mode is “aggfunc”).
min_valid (int) – Minimum number of valid nodes that pass the filter for keeping the RNA (only if aggregation_mode is “min_valid”).

Example

Keep RNAs with at least 1 chemically modified residue:

>>> from rnaglib.dataset import RNADataset
>>> from rnaglib.transforms import ResidueAttributeFilter

>>> dset = RNADataset(debug=True)
>>> t = ResidueAttributeFilter(attribute='is_modified',
                           value_checker: lambda val: val == True,
                           min_valid=1)
>>> len(dset)
>>> rnas = list(t(dset))
>>> len(rnas)

__init__(attribute, aggregation_mode='min_valid', value_checker=None, min_valid=1, aggfunc=None, **kwargs)[source]¶

Methods

`__init__`(attribute[, aggregation_mode, ...])
`forward`(data)	Returns true/ or false on the given RNA