Teicher/DTP converter

thunor/converters/__init__.py

@@ -1,4 +1,6 @@
 from .gdsc import convert_gdsc, convert_gdsc_tags
 from .ctrp2 import convert_ctrp
+from .teicher import convert_teicher
 
-__all__ = ['convert_gdsc', 'convert_gdsc_tags', 'convert_ctrp']
+__all__ = ['convert_gdsc', 'convert_gdsc_tags', 'convert_ctrp',
+           'convert_teicher']

thunor/converters/teicher.py

@@ -0,0 +1,111 @@
+from thunor.io import HtsPandas, write_hdf
+import pandas as pd
+import datetime
+import os
+
+ASSAY = 'lum:Lum'
+TIMEPOINT = datetime.timedelta(hours=96)
+
+FILE_MAIN = 'sclc_export_experiment_dose_resp_element_19FEB2016.csv'
+FILE_CL = 'sclc_export_experiment_19FEB2016.csv'
+FILE_DR = 'sclc_export_compound_19FEB2016.csv'
+
+
+def import_teicher(directory):
+    df = pd.read_csv(os.path.join(directory, FILE_MAIN),
+                     dtype={'concentration': float})
+
+    df_cl = pd.read_csv(os.path.join(directory, FILE_CL),
+                        dtype={'cell_line': str})
+    df = df.merge(df_cl, left_on='experiment_id', right_on='id')
+
+    df_dr = pd.read_csv(os.path.join(directory, FILE_DR),
+                        dtype={'drug_name': str})
+    df = df.merge(df_dr, on='nsc')
+
+    df = df.rename(columns={'cell_line': 'cell.line', 'drug_name': 'drug'})
+
+    df['cell.line'] = df['cell.line'].str.replace('-', '')
+    df['cell.line'] = df['cell.line'].str.replace(' ', '')
+    df['cell.line'] = df['cell.line'].str.strip()
+    df['drug'] = df['drug'].str.strip()
+    df = df.loc[df['drug'] != '', :]
+
+    df['concentration'] = [(d,) for d in df['concentration'].values]
+    df['drug'] = [(d,) for d in df['drug'].values]
+
+    df.rename(columns={
+        'experiment_id': 'plate',
+        'concentration': 'dose',
+        'cell.line': 'cell_line',
+        'mean_pct_ctrl': 'value'
+    }, inplace=True)
+
+    df['well_num'] = df.groupby('plate').cumcount() + 1
+    df['well_id'] = df['plate'].astype(str) + '__' + df['well_num'].astype(str)
+
+    controls_list = []
+    for plate, dat in df.groupby('plate'):
+        cell_lines = dat['cell_line'].unique()
+        assert len(cell_lines == 1)
+        cell_line = cell_lines[0]
+        controls_list.append({
+            'assay': ASSAY,
+            'cell_line': cell_line,
+            'plate': plate,
+            'well_id': '{}__{}'.format(plate, 0),
+            'timepoint': TIMEPOINT,
+            'value': 100.0,
+            'well_num': 0
+        })
+
+    controls = pd.DataFrame(controls_list)
+    controls = controls.set_index(['assay', 'cell_line', 'plate', 'well_id',
+                                   'timepoint'])
+
+    doses = df.loc[:, ['drug', 'cell_line', 'dose', 'well_id', 'plate',
+                       'well_num']]
+    doses = doses.set_index(['drug', 'cell_line', 'dose'])
+
+    assays = df.loc[:, ['well_id', 'value']]
+    assays['timepoint'] = TIMEPOINT
+    assays['assay'] = ASSAY
+    assays = assays.set_index(['assay', 'well_id', 'timepoint'])
+
+    return HtsPandas(doses, assays, controls)
+
+
+def convert_teicher(directory='.', output_file='teicher.h5'):
+    """
+    Convert Teicher data to Thunor format
+
+    The "Teicher" data is a dataset of dose-response data on a panel of
+    small cell lung cancer (SCLC) cell lines. The data can be downloaded from
+    the following link (select the Compound Concentration/Response Data link):
+
+    https://sclccelllines.cancer.gov/sclc/downloads.xhtml
+
+    Unzip the downloaded file. The dataset can then be converted on the command
+    line::
+
+        python -c "from thunor.converters import convert_teicher; convert_teicher()"
+
+    Please note that the layout of wells in each plate after conversion is
+    arbitrary, since this information is not in the original files.
+
+    This will output a file called (by default) :file:`teicher.h5`,
+    which can be opened with :func:`thunor.io.read_hdf()`, or used with Thunor
+    Web.
+
+    Parameters
+    ----------
+    directory: str
+        Directory containing the Teicher dataset
+    output_file: str
+        Filename of output file (Thunor HDF5 format)
+
+    """
+    hts = import_teicher(directory)
+    print('Writing HDF5 file...')
+    write_hdf(hts, output_file)
+    print('Done!')