Add controls example

examples/controls.py

@@ -0,0 +1,62 @@
+import os
+import sys
+import argparse
+from IlluminaBeadArrayFiles import GenotypeCalls, BeadPoolManifest
+
+parser = argparse.ArgumentParser('Generate a control dashboard report')
+parser.add_argument('manifest', help='BPM manifest file')
+parser.add_argument('gtc_directory', help='Directory containing GTC files')
+parser.add_argument('output_file', help='Location to write report')
+
+args = parser.parse_args()
+
+try:
+    manifest = BeadPoolManifest(args.manifest)
+except:
+    sys.stderr.write('Failed to read data from manifest\n')
+    sys.exit(-1)
+
+with open(args.output_file, 'w') as output_handle:
+    # Write header and grab control_config from manifest
+    # Sample_ID and Sentrix_Label may differ from the genome studio report
+    # as we're just using the Sentrix_Label for both in this script
+    output_handle.write(','.join(['Category','Control','BeadType','Sample_ID','Sentrix_Label']))
+    controls = manifest.control_config.split('\n')
+    # Trim empty control if exists
+    if controls[-1] == '':
+        controls.pop(len(controls)-1)
+    num_sections = len(controls[0].split(',')[0].split(':'))
+    for i in range(1, num_sections+1):
+        output_handle.write(',')
+        output_handle.write(','.join([f'Section {i} X', f'Section {i} Y']))
+    output_handle.write('\n')
+
+    # Build controls dictionary from gtcs
+    samples = {}
+    for filename in os.listdir(args.gtc_directory):
+        if filename.lower().endswith('.gtc'):
+            base, ext = os.path.splitext(filename)
+            samples[base] = {'gtc': filename}
+    for sample in samples:
+        sys.stdout.write('Processing ' + sample + '\n')
+        gtc = GenotypeCalls(os.path.join(args.gtc_directory, samples[sample]['gtc']))
+        samples[sample]['controls_x'] = gtc.get_control_x_intensities()
+        samples[sample]['controls_y'] = gtc.get_control_y_intensities()
+
+    # Write out controls in genome studio "ControlDashboard.csv" format
+    sys.stdout.write(f'Writing to {args.output_file}\n')
+    control_offset = 0
+    for control_data in controls:
+        beadtypes, category, color, control = control_data.split(',')
+        # assumes all same beadtype, converts to int then back to str to trim off preceeding zeroes
+        beadtype = str(int(beadtypes.split(':')[0]))
+        for sample in sorted(samples):
+            output_handle.write(','.join([category, control, beadtype, sample, sample]))
+            controls_x = samples[sample]['controls_x'][control_offset:control_offset + num_sections]
+            controls_y = samples[sample]['controls_y'][control_offset:control_offset + num_sections]
+            for x, y in zip(controls_x, controls_y):
+                output_handle.write(',')
+                output_handle.write(f'{x},{y}')
+            output_handle.write('\n')
+        control_offset = control_offset + num_sections
+