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annotate filter.py @ 1:b673449d111a draft default tip

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planemo upload commit f3fb68f4faf6766eef195b8b36157035ab95e7b1-dirty
author yating-l
date Mon, 05 Jun 2017 12:50:14 -0400
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b673449d111a planemo upload commit f3fb68f4faf6766eef195b8b36157035ab95e7b1-dirty
yating-l
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1 import sys
b673449d111a planemo upload commit f3fb68f4faf6766eef195b8b36157035ab95e7b1-dirty
yating-l
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2 import argparse
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yating-l
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3
b673449d111a planemo upload commit f3fb68f4faf6766eef195b8b36157035ab95e7b1-dirty
yating-l
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4 def filter(cds_file, valid_cds_file):
b673449d111a planemo upload commit f3fb68f4faf6766eef195b8b36157035ab95e7b1-dirty
yating-l
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5 valid = open(valid_cds_file, 'w')
b673449d111a planemo upload commit f3fb68f4faf6766eef195b8b36157035ab95e7b1-dirty
yating-l
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6 with open(cds_file, 'r') as f:
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yating-l
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7 for line in f:
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yating-l
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8 if len(line.rstrip().split('\t')) == 2:
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yating-l
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9 valid.write(line)
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yating-l
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10 valid.close()
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11
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yating-l
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12 def main(argv):
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yating-l
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13 parser = argparse.ArgumentParser(description='Filter out records without CDS coordinates')
b673449d111a planemo upload commit f3fb68f4faf6766eef195b8b36157035ab95e7b1-dirty
yating-l
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14 parser.add_argument('-f', help='cds file')
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yating-l
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15 parser.add_argument('-o', help='validated cds file')
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yating-l
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16 args = parser.parse_args()
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yating-l
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17 filter(args.f, args.o)
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18
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yating-l
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19 if __name__ == '__main__':
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yating-l
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20 main(sys.argv)