--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bootstrap.py	Thu Feb 26 18:16:36 2015 -0500
@@ -0,0 +1,84 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+import csv
+import sys
+import os
+import argparse
+
+def warning(*objs):
+    print("WARNING: ", *objs, file=sys.stderr)
+
+def main(arguments):
+
+    parser = argparse.ArgumentParser(arguments, description=__doc__,
+                                     formatter_class=argparse.RawDescriptionHelpFormatter)
+    parser.add_argument('infile', help = "CSV input",
+                        type = argparse.FileType('r'), default = sys.stdin)
+    parser.add_argument('--junior', help = "use junior run specimen naming convention", action = 'store_true')
+    parser.add_argument('--plate', help = "plate number", type = int, required = True)
+    parser.add_argument('--zone', help = "zone number", type = int, required = True)
+    parser.add_argument('--barcodes', help = "name of barcodes file",
+                        type = argparse.FileType('w'), default = 'barcodes.csv')
+    parser.add_argument('--labels', help = "name of labels file",
+                        type = argparse.FileType('w'), default = 'labels.csv')
+    parser.add_argument('--metadata', help = "name of metadata template file",
+                        type = argparse.FileType('w'), default = 'metadata.csv')
+
+    args = parser.parse_args(arguments)
+
+    label_key = 'sampleid'
+    primer_key = 'reverse'
+    barcode_key = 'barcode'
+    zone_key = 'zone'
+
+    fstr = "j{plate_id}{primer_id}" if args.junior else "p{plate_id}z{zone_id}{primer_id}"
+
+    reader = csv.DictReader(sys.stdin)
+
+    barcodes = csv.writer(args.barcodes)
+    labels = csv.writer(args.labels)
+    metadata = csv.writer(args.metadata)
+
+    barcodes.writerow(['stub', 'barcode'])
+    labels.writerow(['specimen', 'label'])
+    metadata.writerow(['specimen', 'plate', 'zone', 'label', 'primer'])
+
+    seen_labels = {}
+    seen_primers = {}
+
+    # TODO: add checks for duplicates, empty fields, etc., and bail if something goes wrong
+    for i, d in enumerate(reader):
+        if not all (k in d for k in (label_key, primer_key, barcode_key)):
+            return "Expected columns not found"
+
+        if zone_key in d and d[zone_key] != str(args.zone):
+            continue
+
+        label = d[label_key]
+        primer = d[primer_key]
+        barcode = d[barcode_key]
+        zone = args.zone
+
+        if not all((label, primer, barcode)):
+            # only print a warning if at least one of the fields is non-empty
+            if any((label, primer, barcode)):
+                warning("Missing required field on row {}, skipping".format(i+2))
+            continue
+
+        if label in seen_labels:
+            return "Duplicate label '{}' found on rows {} and {}".format(label, seen_labels[label]+2, i+2)
+
+        if primer in seen_primers:
+            return "Duplicate primer '{}' found on rows {} and {}".format(primer, seen_primers[primer]+2, i+2)
+
+        seen_labels[label] = i
+        seen_primers[primer] = i
+
+        specimen = fstr.format(plate_id=args.plate, zone_id=zone, primer_id=primer.strip().lower().replace('-',''))
+        barcodes.writerow([specimen, barcode])
+        labels.writerow([specimen, label])
+        metadata.writerow([specimen, args.plate, zone, label, primer])
+
+if __name__ == '__main__':
+    sys.exit(main(sys.argv[1:]))