<jupyter_start><jupyter_text>GoalAccuracy as a function of isotope incorporation & community similarity among replicate microcosms Variable parameters:* shared % of taxa  * 80, 85, 90, 95, 100* permuted % of rank abundances  * 20, 15, 10, 5, 0* atom % isotope incorporation  * **50*** % taxa that incorporate  * 10* n-reps (stocastic: taxon abundances & which incorporate)  * 10   Setting paths<jupyter_code># paths
import os

workDir = '/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/'
buildDir = os.path.join(workDir, 'microBetaDiv')
R_dir = '/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/SIPSimR/scripts/'

fragFile = '/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/ampFrags_kde.pkl'
genome_index = '/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/genome_index.txt'<jupyter_output><empty_output><jupyter_text>Init<jupyter_code>import glob
import itertools
import nestly
%load_ext pushmsg
if not os.path.isdir(buildDir):
    os.makedirs(buildDir)
%cd $buildDir<jupyter_output>/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv<jupyter_text>BD min/max<jupyter_code>## min G+C cutoff
min_GC = 13.5
## max G+C cutoff
max_GC = 80
## max G+C shift
max_13C_shift_in_BD = 0.036


min_BD = min_GC/100.0 * 0.098 + 1.66    
max_BD = max_GC/100.0 * 0.098 + 1.66    

max_BD = max_BD + max_13C_shift_in_BD

print('Min BD: {}'.format(min_BD))
print('Max BD: {}'.format(max_BD))<jupyter_output>Min BD: 1.67323
Max BD: 1.7744<jupyter_text>Nestly<jupyter_code># making an experimental design file for qSIP
x = range(1,7)
y = ['control', 'treatment']

expDesignFile = os.path.join(buildDir, 'qSIP_exp_design.txt')
with open(expDesignFile, 'wb') as outFH:
    for i,z in itertools.izip(x,itertools.cycle(y)):
        line = '\t'.join([str(i),z])
        outFH.write(line + '\n')

!head $expDesignFile<jupyter_output>1	control
2	treatment
3	control
4	treatment
5	control
6	treatment<jupyter_text>Nestly params<jupyter_code># building tree structure
nest = nestly.Nest()


# varying params
nest.add('shared_perc', [80, 85, 90, 95, 100])
nest.add('perm_perc', [0, 5, 10, 15, 20])
nest.add('rep', range(1,11))

## set params
nest.add('percIncorp', [50], create_dir=False)
nest.add('percTaxa', [10], create_dir=False)
nest.add('abs', ['1e9'], create_dir=False)
#nest.add('abs', ['1e7'], create_dir=False)           # TEST
nest.add('np', [10], create_dir=False)
nest.add('Monte_rep', [100000], create_dir=False)
nest.add('subsample_dist', ['lognormal'], create_dir=False)
nest.add('subsample_mean', [9.432], create_dir=False)
nest.add('subsample_scale', [0.5], create_dir=False)
nest.add('subsample_min', [10000], create_dir=False)
nest.add('subsample_max', [30000], create_dir=False)
nest.add('min_BD', [min_BD], create_dir=False)
nest.add('max_BD', [max_BD], create_dir=False)
nest.add('DBL_scaling', [0.5], create_dir=False)
nest.add('bandwidth', [0.8], create_dir=False)
nest.add('heavy_BD_min', [1.71], create_dir=False)
nest.add('heavy_BD_max', [1.75], create_dir=False)
nest.add('topTaxaToPlot', [100], create_dir=False)
nest.add('padj', [0.1], create_dir=False)
nest.add('log2', [0.25], create_dir=False)

### input/output files
nest.add('buildDir', [buildDir], create_dir=False)
nest.add('R_dir', [R_dir], create_dir=False)
nest.add('genome_index', [genome_index], create_dir=False)
nest.add('fragFile', [fragFile], create_dir=False)
nest.add('exp_design', [expDesignFile], create_dir=False)


# building directory tree
nest.build(buildDir)

# bash file to run
bashFile = os.path.join(buildDir, 'SIPSimRun.sh')<jupyter_output><empty_output><jupyter_text>Experimental design<jupyter_code>bashFileTmp = os.path.splitext(bashFile)[0] + '_expDesign.sh'
bashFileTmp
%%writefile $bashFileTmp
#!/bin/bash
source activate SIPSim
# OPENBLAS threads 
export OMP_NUM_THREADS=1

echo '#-- Experimental design --#'

echo '# Making an isotope incorporation config file'
echo '## 3 replicate gradients for control & treatment'
SIPSim incorp_config_example \
  --percIncorpUnif {percIncorp} \
  --n_reps 3 \
  > incorp.config

echo '# Selecting incorporator taxa'
echo '## This is to make the gradient replicates consistent (qSIP finds mean among replicates)'
SIPSim KDE_select_taxa \
    -p {percTaxa} \
    {fragFile} \
    > incorporators.txt

echo '# Creating a community file (3 replicate control, 3 replicate treatment)'
SIPSim communities \
    --richness 950 \
    --config incorp.config \
    --shared_perc {shared_perc} \
    --perm_perc {perm_perc} \
    {genome_index} \
    > comm.txt       

echo '# simulating gradient fractions'
SIPSim gradient_fractions \
    --BD_min {min_BD} \
    --BD_max {max_BD} \
    comm.txt \
    > fracs.txt        
!chmod 755 $bashFileTmp
%%bash -s $workDir $bashFileTmp $buildDir
# offset job start to prevent conda activate errors
sleep $[ ( $RANDOM % 10 )  + 1 ]s
source activate py2_ley0.4
# change to working dir
cd $1
# run job 
nestrun --template-file $2 -d $3 --log-file exp_design.log -j 20
%pushmsg "exp_design complete: $buildDir"<jupyter_output><empty_output><jupyter_text>SIPSim pipeline<jupyter_code>bashFileTmp = os.path.splitext(bashFile)[0] + '_SIPSim-pipeline.sh'
bashFileTmp
%%writefile $bashFileTmp
#!/bin/bash
# offset job start to prevent conda activate errors
sleep $[ ( $RANDOM % 10 )  + 1 ]s
source activate SIPSim
# OPENBLAS threads 
export OMP_NUM_THREADS=1


echo '#-- SIPSim pipeline --#'    
    
echo '# Adding diffusion'    
SIPSim diffusion \
    -n {Monte_rep} \
    --bw {bandwidth} \
    --np {np} \
    {fragFile} \
    > ampFrags_KDE_dif.pkl    

echo '# Adding DBL contamination; abundance-weighted smearing'
SIPSim DBL \
    -n {Monte_rep} \
    --comm comm.txt \
    --commx {DBL_scaling} \
    --np {np} \
    ampFrags_KDE_dif.pkl \
    > ampFrags_KDE_dif_DBL.pkl 

echo '# Adding isotope incorporation to BD distribution'
SIPSim isotope_incorp \
    -n {Monte_rep} \
    --comm comm.txt \
    --taxa incorporators.txt \
    --np {np} \
    ampFrags_KDE_dif_DBL.pkl \
    incorp.config \
    > ampFrags_KDE_dif_DBL_inc.pkl

echo '# Simulating an OTU table'
SIPSim OTU_table \
    --abs {abs} \
    --np {np} \
    ampFrags_KDE_dif_DBL_inc.pkl \
    comm.txt \
    fracs.txt \
    > OTU_abs{abs}.txt
    
echo '# Simulating PCR'
SIPSim OTU_PCR \
    OTU_abs{abs}.txt \
    > OTU_abs{abs}_PCR.txt    
    
echo '# Subsampling from the OTU table (simulating sequencing of the DNA pool)'
SIPSim OTU_subsample \
    --dist {subsample_dist} \
    --dist_params mean:{subsample_mean},sigma:{subsample_scale} \
    --min_size {subsample_min} \
    --max_size {subsample_max} \
    OTU_abs{abs}_PCR.txt \
    > OTU_abs{abs}_PCR_sub.txt
        
echo '# Making a wide-formatted table'
SIPSim OTU_wide_long -w \
    OTU_abs{abs}_PCR_sub.txt \
    > OTU_abs{abs}_PCR_sub_w.txt
    
echo '# Making metadata (phyloseq: sample_data)'
SIPSim OTU_sample_data \
    OTU_abs{abs}_PCR_sub.txt \
    > OTU_abs{abs}_PCR_sub_meta.txt
       

#-- removing large intermediate files --#
rm -f ampFrags_KDE_dif.pkl
rm -f ampFrags_KDE_dif_DBL.pkl
rm -f ampFrags_KDE_dif_DBL_inc.pkl    
!chmod 755 $bashFileTmp
%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

nestrun --template-file $2 -d $3 --log-file SIPSim_pipeline.log -j 6 --stop-on-error
%pushmsg "SIPSim pipeline complete: $buildDir"<jupyter_output><empty_output><jupyter_text>Summary of simulated data<jupyter_code>bashFileTmp = os.path.splitext(bashFile)[0] + '_SIPSim-summary.sh'
bashFileTmp
%%writefile $bashFileTmp
#!/bin/bash
# offset job start to prevent conda activate errors
sleep $[ ( $RANDOM % 10 )  + 1 ]s
source activate SIPSim 

echo "# Plotting taxon abundances"

# plotting 'raw' taxon abundances
Rscript {R_dir}OTU_taxonAbund.R \
    OTU_abs{abs}.txt \
    -r {topTaxaToPlot} \
    -o OTU_abs{abs}

# plotting 'sequenced' taxon abundances
Rscript {R_dir}OTU_taxonAbund.R \
    OTU_abs{abs}_PCR_sub.txt \
    -r {topTaxaToPlot} \
    -o OTU_abs{abs}_PCR_sub
!chmod 755 $bashFileTmp
%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

nestrun --template-file $2 -d $3 --log-file SIPSim_summary.log -j 20<jupyter_output><empty_output><jupyter_text>HR-SIP<jupyter_code>bashFileTmp = os.path.splitext(bashFile)[0] + '_HRSIP.sh'
bashFileTmp
%%writefile $bashFileTmp
#!/bin/bash
# offset job start to prevent conda activate errors
sleep $[ ( $RANDOM % 10 )  + 1 ]s
source activate SIPSim 

# phyloseq
## making phyloseq object from OTU table
Rscript {R_dir}phyloseq_make.R \
    OTU_abs{abs}_PCR_sub_w.txt \
    -s OTU_abs{abs}_PCR_sub_meta.txt \
    > OTU_abs{abs}_PCR_sub.physeq

## filtering phyloseq object to just 'heavy' fractions
Rscript {R_dir}phyloseq_edit.R \
    OTU_abs{abs}_PCR_sub.physeq \
    --BD_min {heavy_BD_min} \
    --BD_max {heavy_BD_max} \
    > OTU_abs{abs}_PCR_sub_filt.physeq

## making ordination
Rscript {R_dir}phyloseq_ordination.R \
    OTU_abs{abs}_PCR_sub_filt.physeq \
    OTU_abs{abs}_PCR_sub_filt_bray-NMDS.pdf

# DESeq2
Rscript {R_dir}phyloseq_DESeq2.R \
    --log2 {log2} \
    --hypo greater \
    --cont 1,3,5 \
    --treat 2,4,6 \
    OTU_abs{abs}_PCR_sub_filt.physeq \
    > OTU_abs{abs}_PCR_sub_filt_DESeq2
!chmod 755 $bashFileTmp
%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

nestrun --template-file $2 -d $3 --log-file HR-SIP.log -j 20
%pushmsg "HR-SIP complete: $buildDir"<jupyter_output><empty_output><jupyter_text>MW-HR-SIP<jupyter_code>bashFileTmp = os.path.splitext(bashFile)[0] + '_MWHRSIP.sh'
bashFileTmp
%%writefile $bashFileTmp
#!/bin/bash
# offset job start to prevent conda activate errors
sleep $[ ( $RANDOM % 10 )  + 1 ]s
source activate SIPSim 

## HR SIP pipeline
Rscript {R_dir}phyloseq_DESeq2.R \
    --log2 {log2} \
    --hypo greater \
    --cont 1,3,5 \
    --treat 2,4,6 \
    --occur_all 0.0,0.05,0.1,0.15,0.2,0.25,0.3,0.35,0.4,0.45,0.5 \
    -w 1.70-1.73,1.72-1.75,1.74-1.77 \
    --all OTU_abs1e9_PCR_sub_MW-all.txt \
    OTU_abs{abs}_PCR_sub.physeq \
    > OTU_abs{abs}_PCR_sub_filt_MW_DESeq2
!chmod 755 $bashFileTmp
%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

nestrun --template-file $2 -d $3 --log-file MW-HR-SIP.log -j 20
%pushmsg "MW-HR-SIP complete: $buildDir"<jupyter_output><empty_output><jupyter_text>q-SIP<jupyter_code>bashFileTmp = os.path.splitext(bashFile)[0] + '_qSIP.sh'
bashFileTmp
%%writefile $bashFileTmp
#!/bin/bash
# offset job start to prevent conda activate errors
sleep $[ ( $RANDOM % 10 )  + 1 ]s
source activate SIPSim 
# OPENBLAS threads 
export OMP_NUM_THREADS=1

# qSIP
SIPSim qSIP \
    OTU_abs{abs}.txt \
    OTU_abs{abs}_PCR_sub.txt \
    > OTU_abs{abs}_PCR_sub_qSIP.txt
        

# qSIP: atom excess
SIPSim qSIP_atom_excess \
    --np {np} \
    OTU_abs{abs}_PCR_sub_qSIP.txt \
    {exp_design} \
    > OTU_abs{abs}_PCR_sub_qSIP_atom.txt  
!chmod 755 $bashFileTmp
%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

nestrun --template-file $2 -d $3 --log-file qSIP.log -j 6
%pushmsg "q-SIP complete: $buildDir"<jupyter_output><empty_output><jupyter_text>delta-BD<jupyter_code>bashFileTmp = os.path.splitext(bashFile)[0] + '_dBD.sh'
bashFileTmp
%%writefile $bashFileTmp
#!/bin/bash
# offset job start to prevent conda activate errors
sleep $[ ( $RANDOM % 10 )  + 1 ]s
source activate SIPSim 
# OPENBLAS threads 
export OMP_NUM_THREADS=1

#deltaBD 
SIPSim deltaBD \
    OTU_abs{abs}_PCR_sub.txt \
    {exp_design} \
    > OTU_abs{abs}_PCR_sub_dBD.txt  
!chmod 755 $bashFileTmp
%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

nestrun --template-file $2 -d $3 --log-file deltaBD.log -j 20
%pushmsg "deltaBD complete: $buildDir"<jupyter_output><empty_output><jupyter_text>Making confusion matrices<jupyter_code>bashFileTmp = os.path.splitext(bashFile)[0] + '_cMtx.sh'
bashFileTmp
%%writefile $bashFileTmp
#!/bin/bash
# offset job start to prevent conda activate errors
sleep $[ ( $RANDOM % 10 )  + 1 ]s
source activate SIPSim

# HR-SIP
Rscript {R_dir}DESeq2_confuseMtx.R \
    --libs 2,4,6 \
    --padj {padj} \
    BD-shift_stats.txt \
    OTU_abs{abs}_PCR_sub_filt_DESeq2

# HR-SIP multiple 'heavy' BD windows
Rscript {R_dir}DESeq2_confuseMtx.R \
    --libs 2,4,6 \
    --padj {padj} \
    -o DESeq2_multi-cMtx \
    BD-shift_stats.txt \
    OTU_abs{abs}_PCR_sub_filt_MW_DESeq2
    
# qSIP    
Rscript {R_dir}qSIP_confuseMtx.R \
    --libs 2,4,6 \
    BD-shift_stats.txt \
    OTU_abs{abs}_PCR_sub_qSIP_atom.txt

# heavy-SIP    
Rscript {R_dir}heavy_confuseMtx.R \
    --treat 2,4,6 \
    --con 1,3,5 \
    --method 1 \
    BD-shift_stats.txt \
    OTU_abs{abs}_PCR_sub.txt
!chmod 755 $bashFileTmp
%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

nestrun --template-file $2 -d $3 --log-file cMtx.log -j 20<jupyter_output><empty_output><jupyter_text>Aggregating confusion matrices<jupyter_code>def agg_cMtx(prefix):
    # all data
    x = prefix + '-cMtx_data.txt'
    !nestagg delim \
       -d $buildDir \
       -k shared_perc,perm_perc,rep \
       -o $x \
       --tab \
       $x

    # overall
    x = prefix + '-cMtx_overall.txt'
    !nestagg delim \
        -d $buildDir \
        -k shared_perc,perm_perc,rep \
        -o $x \
        --tab \
        $x

    # by class
    x = prefix + '-cMtx_byClass.txt'
    !nestagg delim \
        -d $buildDir \
        -k shared_perc,perm_perc,rep \
        -o $x \
        --tab \
        $x
        
agg_cMtx('DESeq2')
agg_cMtx('DESeq2_multi')
agg_cMtx('qSIP') 
agg_cMtx('heavy') 
%pushmsg "microBetaDiv complete!"<jupyter_output><empty_output><jupyter_text>Calculating pre-fractionation comm beta-div indices<jupyter_code>bashFileTmp = os.path.splitext(bashFile)[0] + '_betaDiv.sh'
bashFileTmp
%%writefile $bashFileTmp
#!/bin/bash
source activate SIPSim

# beta diversity
Rscript {R_dir}comm_beta_div.R \
    comm.txt \
    > comm_betaDiv.txt
!chmod 755 $bashFileTmp
%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

nestrun --template-file $2 -d $3 --log-file comm_betaDiv.log -j 10<jupyter_output>2017-08-20 20:09:43,185 * INFO * Template: ./SIPSimRun_betaDiv.sh
2017-08-20 20:09:43,190 * INFO * [71028] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/1
2017-08-20 20:09:43,195 * INFO * [71031] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/2
2017-08-20 20:09:43,202 * INFO * [71039] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/3
2017-08-20 20:09:43,208 * INFO * [71046] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/4
2017-08-20 20:09:43,214 * INFO * [71057] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/5
2017-08-20 20:09:43,220 * INFO * [71065] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanoge[...]<jupyter_text>--End of simulation-- ***  Results<jupyter_code>F = os.path.join(buildDir, '*-cMtx_byClass.txt')
files = glob.glob(F)
files
# checking for errors
!find $buildDir -name "*log" | wc -l
!find $buildDir -name "*log" | xargs grep -i error<jupyter_output>2250
{'fraction_non_alphanumeric': 0.13386750048856752, 'fraction_numerical': 0.03999739430655983, 'mean_word_length': 3.94110074026392, 'pattern_counts': {'":': 0, '<': 60, '<?xml version=': 0, '>': 80, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'chain_length': '16', 'dir': 'jupyter-structured-clean-dedup', 'id': '133979', 'license': 'MIT', 'n_tokens_mistral': 6966, 'n_tokens_neox': 6285, 'n_words': 1219, 'path': 'ipynb/bac_genome/n1147_pt2/microBetaDiv.ipynb', 'repo_name': 'arischwartz/test', 'size': '15351'}