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1 import sys, os
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2 import parseFasta
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3
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4 # Create OTU Table
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5 # OTU_Lable | Count | Sequence
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6 #
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7 # Author: Anne Kunert
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8 #
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9
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10 OTUmap = sys.argv[1]
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11 OTUcount = sys.argv[2]
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12
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13 def transform(file):
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14 seq = parseFasta.FastaParser(OTUmap)
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15 with open(file) as f:
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16 lis=[x.split() for x in f]
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17 end=""
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18 line=""
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19 myseq=""
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20 for x in zip(*lis):
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21 otu_lable = x[0]
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22 for item in seq:
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23 if item == otu_lable:
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24 myseq = seq.records[item]['sequence']
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25 myseq = myseq.replace('\n','')
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26 for y in x:
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27 line= line+str(y)+"\t"
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28 print(line+myseq)
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29 line=""
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30 myseq=""
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31
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32 transform(OTUcount)
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