Mercurial > repos > qfab > rdp_multiclassifier
comparison rdpmulticlassifier/scripts/.svn/text-base/generateOTUtable.py.svn-base @ 0:a73ae72b47aa draft default tip
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author | qfab |
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date | Thu, 29 May 2014 02:27:56 -0400 |
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-1:000000000000 | 0:a73ae72b47aa |
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1 # create OTU Table by merging pre otu table with taxonomy assign by | |
2 # rdpmulticlassifier | |
3 # Tab-separated fields: | |
4 # 1=OTU Label, 2=Count, 3=Sequence, 4 and following=Assigned taxonomy by | |
5 # RDP Multi Classifier | |
6 | |
7 import sys, os | |
8 | |
9 OTUtable = sys.argv[1] | |
10 PreOTUtable = sys.argv[2] | |
11 RdpTaxonomy = sys.argv[3] | |
12 | |
13 def merge(output, preotu, tax): | |
14 writeoutput = open(output, 'w') | |
15 lookup = {} | |
16 with open(tax) as f: | |
17 for x in f: | |
18 list = x.split('\t') | |
19 length = len(list) | |
20 rest ='' | |
21 for k in range(1, length): | |
22 item= list[k].replace(' ','') | |
23 item= item.replace('\n','') | |
24 rest = rest+ item + '\t' | |
25 lookup[list[0]] = rest | |
26 with open(preotu) as f: | |
27 for x in f: | |
28 columns = x.split('\t') | |
29 otu = columns[0].replace(' ','') | |
30 taxonomy = lookup[otu] | |
31 line = x.replace('\n','') | |
32 writeoutput.write(line+taxonomy+'\n') | |
33 | |
34 merge(OTUtable, PreOTUtable, RdpTaxonomy) |