Copy corrections is based on copyrighter. One copy database for each Greengene taxon at each level is provided by the tool. We will use that database for correcting our Greengene taxonomy abundance and OTU abundance.



In [28]:

    
cd /usr/local/notebooks









    



/usr/local/notebooks



In [29]:

    
### set up directory
!mkdir -p ./workdir/copy_correction



In [30]:

    
Prefix='SS'    # name for the analysis run
Script_dir='./SSUsearch/scripts'
Wkdir='./workdir'
Design='./data/test/SS.design'
Otu_dist_cutoff='0.05'
Copy_db='./data/SSUsearch_db/Copy_db.copyrighter.txt'



In [31]:

    
import os
Script_dir=os.path.abspath(Script_dir)
Wkdir=os.path.abspath(Wkdir)
Design=os.path.abspath(Design)
Copy_db=os.path.abspath(Copy_db)

os.environ.update(
    {'Prefix':Prefix,
     'Script_dir': Script_dir, 
     'Wkdir': Wkdir, 
     'Otu_dist_cutoff':Otu_dist_cutoff,
     'Design': Design, 
     'Copy_db': Copy_db})



In [32]:

    
cd ./workdir/copy_correction









    



/usr/local/notebooks/workdir/copy_correction



In [33]:

    
# get input files from '/usr/local/notebooks/workdir/clust'
!ln -sf $Wkdir/clust/$Prefix.biom
!ln -sf $Wkdir/clust/$Prefix.list



In [34]:

    
# get Greengene taxonomy
!cat $Wkdir/*.ssu.out/*.gg.taxonomy > $Prefix.taxonomy
!mothur "#classify.otu(list=$Prefix.list, taxonomy=$Prefix.taxonomy, label=$Otu_dist_cutoff)"
!mv SS.0.03.cons.taxonomy SS.cons.taxonomy
!mv SS.0.03.cons.tax.summary SS.cons.tax.summary









    








mothur v.1.34.4
Last updated: 12/22/2014

by
Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

Type 'quit()' to exit program



mothur > classify.otu(list=SS.list, taxonomy=SS.taxonomy, label=0.05)
reftaxonomy is not required, but if given will keep the rankIDs in the summary file static.
Your file does not include the label 0.05. I will use 0.03.
0.03	147

Output File Names: 
SS.0.03.cons.taxonomy
SS.0.03.cons.tax.summary


mothur > quit()



In [35]:

    
!mothur "#make.shared(biom=$Prefix.biom)"

# do copy correction and even sampling
!python $Script_dir/copyrighter-otutable.py $Copy_db \
    $Prefix.cons.taxonomy \
    $Prefix.shared $Prefix.cc.shared
    
!mv $Prefix.cc.shared $Prefix.shared
!mothur "#make.biom(shared=$Prefix.shared, constaxonomy=$Prefix.cons.taxonomy);"
!mv $Prefix.userLabel.biom $Prefix.biom
!rm -f mothur.*.logfile









    








mothur v.1.34.4
Last updated: 12/22/2014

by
Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

Type 'quit()' to exit program



mothur > make.shared(biom=SS.biom)

userLabel

Output File Names: 
SS.shared
SS.1c.rabund
SS.1d.rabund
SS.2c.rabund
SS.2d.rabund


mothur > quit()






mothur v.1.34.4
Last updated: 12/22/2014

by
Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

Type 'quit()' to exit program



mothur > make.biom(shared=SS.shared, constaxonomy=SS.cons.taxonomy)
userLabel

Output File Names: 
SS.userLabel.biom


mothur > quit()

SS.biom can be further used for diversity analysis, important but not focus of this tutorial (details see mothur wiki).



In [36]:

    
!mothur "#make.shared(biom=$Prefix.biom); sub.sample(shared=$Prefix.shared); summary.single(calc=nseqs-coverage-sobs-chao-shannon-invsimpson); dist.shared(calc=braycurtis); pcoa(phylip=$Prefix.userLabel.subsample.braycurtis.userLabel.lt.dist); nmds(phylip=$Prefix.userLabel.subsample.braycurtis.userLabel.lt.dist); amova(phylip=$Prefix.userLabel.subsample.braycurtis.userLabel.lt.dist, design=$Design); tree.shared(calc=braycurtis); unifrac.weighted(tree=$Prefix.userLabel.subsample.braycurtis.userLabel.tre, group=$Design, random=T)"
!rm -f mothur.*.logfile; 
!rm -f *.rabund









    








mothur v.1.34.4
Last updated: 12/22/2014

by
Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

Type 'quit()' to exit program



mothur > make.shared(biom=SS.biom)

userLabel

Output File Names: 
SS.shared
SS.1c.rabund
SS.1d.rabund
SS.2c.rabund
SS.2d.rabund


mothur > sub.sample(shared=SS.shared)
Sampling 7 from each group.
userLabel

Output File Names: 
SS.userLabel.subsample.shared


mothur > summary.single(calc=nseqs-coverage-sobs-chao-shannon-invsimpson)
Using SS.userLabel.subsample.shared as input file for the shared parameter.

Processing group 1c

userLabel

Processing group 1d

userLabel

Processing group 2c

userLabel

Processing group 2d

userLabel

Output File Names: 
SS.userLabel.subsample.groups.summary


mothur > dist.shared(calc=braycurtis)
Using SS.userLabel.subsample.shared as input file for the shared parameter.

Using 1 processors.
userLabel

Output File Names: 
SS.userLabel.subsample.braycurtis.userLabel.lt.dist


mothur > pcoa(phylip=SS.userLabel.subsample.braycurtis.userLabel.lt.dist)

Processing...
Rsq 1 axis: 0.4
Rsq 2 axis: 0.989613
Rsq 3 axis: 1

Output File Names: 
SS.userLabel.subsample.braycurtis.userLabel.lt.pcoa.axes
SS.userLabel.subsample.braycurtis.userLabel.lt.pcoa.loadings


mothur > nmds(phylip=SS.userLabel.subsample.braycurtis.userLabel.lt.dist)
Processing Dimension: 2
1
2
3
4
5
6
7
8
9
10

Number of dimensions:	2
Lowest stress :	0.152963
R-squared for configuration:	0.360718

Output File Names: 
SS.userLabel.subsample.braycurtis.userLabel.lt.nmds.iters
SS.userLabel.subsample.braycurtis.userLabel.lt.nmds.stress
SS.userLabel.subsample.braycurtis.userLabel.lt.nmds.axes


mothur > amova(phylip=SS.userLabel.subsample.braycurtis.userLabel.lt.dist, design=/usr/local/notebooks/data/test/SS.design)
c-d	Among	Within	Total
SS	0.433674	1	1.43367
df	1	2	3
MS	0.433674	0.5

Fs:	0.867347
p-value: 1

Experiment-wise error rate: 0.05
If you have borderline P-values, you should try increasing the number of iterations

Output File Names: 
SS.userLabel.subsample.braycurtis.userLabel.lt.amova


mothur > tree.shared(calc=braycurtis)
Using SS.userLabel.subsample.shared as input file for the shared parameter.

Using 1 processors.
userLabel

Output File Names: 
SS.userLabel.subsample.braycurtis.userLabel.tre


mothur > unifrac.weighted(tree=SS.userLabel.subsample.braycurtis.userLabel.tre, group=/usr/local/notebooks/data/test/SS.design, random=T)

Using 1 processors.
Tree#	Groups	WScore	WSig
1	c-d	0.928571	<0.0010
It took 0 secs to run unifrac.weighted.

Output File Names: 
SS.userLabel.subsample.braycurtis.userLabel.trewsummary
SS.userLabel.subsample.braycurtis.userLabel.tre1.weighted


mothur > quit()



In [ ]: