class jade.nnk.NNKAbMaturation.GetNNKData(data_dir, ab_group='glCHA31')

Bases: object

Get NNK Data as a formatted tupple of 1d data (Or raw Pandas DF)

get_1d_data_tuple_freq_nnk_data(antigen='C5-SOSIP', sort='S1')

get_2D_data_freq_nnk_data(antigen='C5-SOSIP', sort='S1')

Return a dataframe with ResType as index and resnum as columns. :param antigen: :param sort: :rtype: pandas.DataFrame

get_nnk_data(dt='freqTopPerPosition', antigen='C5-SOSIP', sort='S1')

Get pandas dataframe of NNK data.

reinit(ab_class)

jade.nnk.NNKAbMaturation.load_1d_data(data_dir, data_type)

Here, this is a test bed for SVM and simple neural networks No recurrent Neural nets or anything fancy. Will have to try that next.

The 1D data is so that the residuetypes all line up in the SVM. :param data_dir: :return:

jade.nnk.NNKAbMaturation.load_2d_data(data_dir, data_type)

Load a representation of the 2D data with res and position.

Parameters:data_dir – Returns:

jade.nnk.NNKAbMaturation.write_raw_sorts(data, outdir, outname='raw_enrichments.csv', antigen='GT81')

Write the data as columns, S1, S2, S3 for easy import into matlab.

Parameters:

• data –
• outdir –
• outname –
• antigen –

Returns: