updated dev gui scripts and new template

tests/dev_gui_simulated.py

@@ -20,6 +20,7 @@
 
 fpath = os.path.join(directory, 'test_data', 'simulated_data.csv')
 data = np_from_txt(fpath, delimiter=',')
+data['end'] += 1
 uptake = np.zeros_like(data, dtype=float)
 data = append_fields(data, 'uptake', data=uptake, usemask=False)
 sequence = 'XXXXTPPRILALSAPLTTMMFSASALAPKIXXXXLVIPWINGDKG'
@@ -29,14 +30,22 @@
 nc_start, nc_end = 31, 34  # span of no coverage area (inc, inc)
 
 pmt = PeptideMasterTable(data, drop_first=1, ignore_prolines=True, remove_nan=False)
+
+uptake_corrected = pmt.data['scores'] * pmt.data['ex_residues']
+pmt.data = append_fields(pmt.data, ['uptake_corrected'], [uptake_corrected])
+
+
 states = pmt.groupby_state()
 series = states['state1']
+series.make_uniform()
 
 kf = KineticsFitting(series, bounds=(1e-2, 800))
 
 ctrl = Controller('template', ['asdf'])
 ctrl.series = series
 
+print(ctrl.series.tf_cov)
+
 pickle_names = ['fit_simulated_wt_avg', 'fit_simulated_blocks', 'fit_simulated_rates', 'fit_simulated_pfact']
 fit_results = []
 

tests/load_ds1_template.py

@@ -0,0 +1,18 @@
+from pyhdx.fileIO import read_dynamx
+from pyhdx import PeptideMasterTable
+import os
+
+directory = os.path.dirname(__file__)
+fpath = os.path.join(directory, 'test_data', 'ds1.csv')
+
+data_dir = r'../data'
+state = 'PpiANative'
+control = ('PpiA-FD', 0.167)
+
+data = read_dynamx(fpath)
+
+pf = PeptideMasterTable(data, drop_first=1, ignore_prolines=True, remove_nan=False)
+pf.set_control(control)
+states = pf.groupby_state()
+series = states[state]
+series.make_uniform()