view rdpmulticlassifier/scripts/.svn/text-base/generateOTUtable.py.svn-base @ 0:a73ae72b47aa draft default tip

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−# create OTU Table by merging pre otu table with taxonomy assign by
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−# rdpmulticlassifier
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−# Tab-separated fields:
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−# 1=OTU Label, 2=Count, 3=Sequence, 4 and following=Assigned taxonomy by
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−# RDP Multi Classifier
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−
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−import sys, os
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−
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−OTUtable = sys.argv[1]
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−PreOTUtable = sys.argv[2]
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−RdpTaxonomy = sys.argv[3]
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−
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−def merge(output, preotu, tax):
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−    writeoutput = open(output, 'w')
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−    lookup = {} 
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−    with open(tax) as f:
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−        for x in f:
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−	    list = x.split('\t')
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−            length = len(list)
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−	    rest =''
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−            for k in range(1, length):
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−                item= list[k].replace(' ','') 
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−                item= item.replace('\n','')
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−            	rest = rest+ item + '\t'
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−	    lookup[list[0]] = rest
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−    with open(preotu) as f:
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−	for x in f:
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−	    columns = x.split('\t')
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−            otu = columns[0].replace(' ','')         
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−            taxonomy = lookup[otu]
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−            line = x.replace('\n','')
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−	    writeoutput.write(line+taxonomy+'\n')
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−
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−merge(OTUtable, PreOTUtable, RdpTaxonomy)