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1 import csv
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2 import sys
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3
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4 __author__ = "Marcel Kempenaar"
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5 __contact__ = "brs@nbic.nl"
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6 __copyright__ = "Copyright, 2012, Netherlands Bioinformatics Centre"
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7 __license__ = "MIT"
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8
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9 in_file = sys.argv[1]
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10 out_file = sys.argv[2]
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11 to_select_list = [str(select.strip()) for select in sys.argv[3].split(',') if (len(select) > 0)]
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12
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13 data = list(csv.reader(open(in_file, 'rb'), delimiter='\t'))
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14 header = data.pop(0)
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15 header_clean = [i.lower().strip().replace(".", "").replace("%", "") for i in header]
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16 rank = header_clean.index("rank")
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17
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18 writer = csv.writer(open(out_file, 'wb'), delimiter='\t')
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19 writer.writerow(header)
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20 for select in to_select_list:
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21 writer.writerows([i for i in data if i[rank] == select])
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