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1 #!/usr/bin/env python
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2
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3 from __future__ import print_function
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4 import csv
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5 import sys
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6 import os
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7 import argparse
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8
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9 def warning(*objs):
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10 print("WARNING: ", *objs, file=sys.stderr)
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11
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12 def main(arguments):
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13
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14 parser = argparse.ArgumentParser(arguments, description=__doc__,
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15 formatter_class=argparse.RawDescriptionHelpFormatter)
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16 parser.add_argument('infile', help = "CSV input",
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17 type = argparse.FileType('r'), default = sys.stdin)
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18 parser.add_argument('--junior', help = "use junior run specimen naming convention", action = 'store_true')
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19 parser.add_argument('--plate', help = "plate number", type = int, required = True)
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20 parser.add_argument('--zone', help = "zone number", type = int, required = True)
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21 parser.add_argument('--barcodes', help = "name of barcodes file",
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22 type = argparse.FileType('w'), default = 'barcodes.csv')
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23 parser.add_argument('--labels', help = "name of labels file",
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24 type = argparse.FileType('w'), default = 'labels.csv')
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25 parser.add_argument('--metadata', help = "name of metadata template file",
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26 type = argparse.FileType('w'), default = 'metadata.csv')
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27
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28 args = parser.parse_args(arguments)
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29
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30 label_key = 'sampleid'
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31 primer_key = 'reverse'
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32 barcode_key = 'barcode'
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33 zone_key = 'zone'
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34
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35 fstr = "j{plate_id}{primer_id}" if args.junior else "p{plate_id}z{zone_id}{primer_id}"
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36
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37 reader = csv.DictReader(sys.stdin)
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38
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39 barcodes = csv.writer(args.barcodes)
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40 labels = csv.writer(args.labels)
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41 metadata = csv.writer(args.metadata)
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42
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43 barcodes.writerow(['stub', 'barcode'])
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44 labels.writerow(['specimen', 'label'])
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45 metadata.writerow(['specimen', 'plate', 'zone', 'label', 'primer'])
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46
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47 seen_labels = {}
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48 seen_primers = {}
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49
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50 # TODO: add checks for duplicates, empty fields, etc., and bail if something goes wrong
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51 for i, d in enumerate(reader):
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52 if not all (k in d for k in (label_key, primer_key, barcode_key)):
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53 return "Expected columns not found"
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54
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55 if zone_key in d and d[zone_key] != str(args.zone):
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56 continue
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57
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58 label = d[label_key]
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59 primer = d[primer_key]
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60 barcode = d[barcode_key]
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61 zone = args.zone
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62
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63 if not all((label, primer, barcode)):
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64 # only print a warning if at least one of the fields is non-empty
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65 if any((label, primer, barcode)):
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66 warning("Missing required field on row {}, skipping".format(i+2))
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67 continue
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68
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69 if label in seen_labels:
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70 return "Duplicate label '{}' found on rows {} and {}".format(label, seen_labels[label]+2, i+2)
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71
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72 if primer in seen_primers:
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73 return "Duplicate primer '{}' found on rows {} and {}".format(primer, seen_primers[primer]+2, i+2)
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74
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75 seen_labels[label] = i
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76 seen_primers[primer] = i
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77
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78 specimen = fstr.format(plate_id=args.plate, zone_id=zone, primer_id=primer.strip().lower().replace('-',''))
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79 barcodes.writerow([specimen, barcode])
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80 labels.writerow([specimen, label])
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81 metadata.writerow([specimen, args.plate, zone, label, primer])
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82
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83 if __name__ == '__main__':
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84 sys.exit(main(sys.argv[1:]))
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