annotate 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
# rdpmulticlassifier
# Tab-separated fields:
# 1=OTU Label, 2=Count, 3=Sequence, 4 and following=Assigned taxonomy by
# RDP Multi Classifier

import sys, os

OTUtable = sys.argv[1]
PreOTUtable = sys.argv[2]
RdpTaxonomy = sys.argv[3]

def merge(output, preotu, tax):
    writeoutput = open(output, 'w')
    lookup = {} 
    with open(tax) as f:
        for x in f:
	    list = x.split('\t')
            length = len(list)
	    rest =''
            for k in range(1, length):
                item= list[k].replace(' ','') 
                item= item.replace('\n','')
            	rest = rest+ item + '\t'
	    lookup[list[0]] = rest
    with open(preotu) as f:
	for x in f:
	    columns = x.split('\t')
            otu = columns[0].replace(' ','')         
            taxonomy = lookup[otu]
            line = x.replace('\n','')
	    writeoutput.write(line+taxonomy+'\n')

merge(OTUtable, PreOTUtable, RdpTaxonomy)