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import os
import glob
import itertools
import nestly
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%load_ext rpy2.ipython
%load_ext pushnote
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%%R
library(ggplot2)
library(dplyr)
library(tidyr)
library(gridExtra)
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## 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)
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# paths
workDir = '/home/nick/notebook/SIPSim/dev/bac_genome1147/'
buildDir = os.path.join(workDir, 'atomIncorp_taxaIncorp_rerun')
R_dir = '/home/nick/notebook/SIPSim/lib/R/'
fragFile = '/home/nick/notebook/SIPSim/dev/bac_genome1147/validation/ampFrags_kde.pkl'
genome_index = '/var/seq_data/ncbi_db/genome/Jan2016/bac_complete_spec-rep1_rn/genome_index.txt'
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if not os.path.isdir(buildDir):
os.makedirs(buildDir)
%cd $buildDir
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# 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
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# building tree structure
nest = nestly.Nest()
# varying params: test
nest.add('percIncorp', [100])
nest.add('percTaxa', [10])
nest.add('rep', range(1,3))
# varying params
#nest.add('percIncorp', [0, 25, 50, 100])
#nest.add('percTaxa', [1, 5, 10, 25, 50])
#nest.add('rep', range(1,11))
## set params
nest.add('abs', ['1e9'], create_dir=False)
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')
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bashFileTmp = os.path.splitext(bashFile)[0] + '_expDesign.sh'
bashFileTmp
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%%writefile $bashFileTmp
#!/bin/bash
echo '#-- Experimental design --#'
echo '# Making an isotope incorporation config file'
echo '## 3 replicate gradients for control & treatment'
SIPSim incorpConfigExample \
--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_selectTaxa \
-p {percTaxa} \
{fragFile} \
> incorporators.txt
echo '# Creating a community file (3 replicate control, 3 replicate treatment)'
SIPSim communities \
--config incorp.config \
{genome_index} \
> comm.txt
echo '# simulating gradient fractions'
SIPSim gradient_fractions \
--BD_min {min_BD} \
--BD_max {max_BD} \
comm.txt \
> fracs.txt
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!chmod 777 $bashFileTmp
!cd $workDir; \
nestrun --template-file $bashFileTmp -d $buildDir --log-file exp_design.log -j 10
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%pushnote exp_design complete: $buildDir
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bashFileTmp = os.path.splitext(bashFile)[0] + '_SIPSim-pipeline.sh'
bashFileTmp
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%%writefile $bashFileTmp
#!/bin/bash
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_wideLong -w \
OTU_abs{abs}_PCR_sub.txt \
> OTU_abs{abs}_PCR_sub_w.txt
echo '# Making metadata (phyloseq: sample_data)'
SIPSim OTU_sampleData \
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
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!chmod 777 $bashFileTmp
!cd $workDir; \
nestrun --template-file $bashFileTmp -d $buildDir --log-file SIPSim_pipeline.log -j 2
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%pushnote SIPSim pipeline complete: $buildDir
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bashFileTmp = os.path.splitext(bashFile)[0] + '_SIPSim-summary.sh'
bashFileTmp
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%%writefile $bashFileTmp
#!/bin/bash
# plotting 'raw' taxon abundances
SIPSimR OTU_taxonAbund \
OTU_abs{abs}.txt \
-r {topTaxaToPlot} \
-o OTU_abs{abs}
# plotting 'sequenced' taxon abundances
SIPSimR OTU_taxonAbund \
OTU_abs{abs}_PCR_sub.txt \
-r {topTaxaToPlot} \
-o OTU_abs{abs}_PCR_sub
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!chmod 777 $bashFileTmp
!cd $workDir; \
nestrun --template-file $bashFileTmp -d $buildDir --log-file SIPSim_summary.log -j 10
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bashFileTmp = os.path.splitext(bashFile)[0] + '_HRSIP.sh'
bashFileTmp
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%%writefile $bashFileTmp
#!/bin/bash
# phyloseq
## making phyloseq object from OTU table
SIPSimR phyloseq_make \
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
SIPSimR phyloseq_edit \
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
SIPSimR phyloseq_ordination \
OTU_abs{abs}_PCR_sub_filt.physeq \
OTU_abs{abs}_PCR_sub_filt_bray-NMDS.pdf
# DESeq2
SIPSimR phyloseq_DESeq2 \
--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
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!chmod 777 $bashFileTmp
!cd $workDir; \
nestrun --template-file $bashFileTmp -d $buildDir --log-file HR-SIP.log -j 10
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%pushnote HR-SIP complete: $buildDir
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bashFileTmp = os.path.splitext(bashFile)[0] + '_qSIP.sh'
bashFileTmp
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%%writefile $bashFileTmp
#!/bin/bash
# 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_atomExcess \
--np {np} \
OTU_abs{abs}_PCR_sub_qSIP.txt \
{exp_design} \
> OTU_abs{abs}_PCR_sub_qSIP_atom.txt
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!chmod 777 $bashFileTmp
!cd $workDir; \
nestrun --template-file $bashFileTmp -d $buildDir --log-file qSIP.log -j 2
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%pushnote qSIP complete: $buildDir
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bashFileTmp = os.path.splitext(bashFile)[0] + '_cMtx.sh'
bashFileTmp
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%%writefile $bashFileTmp
#!/bin/bash
SIPSimR DESeq2_confuseMtx \
--libs 2,4,6 \
--padj {padj} \
BD-shift_stats.txt \
OTU_abs{abs}_PCR_sub_filt_DESeq2
SIPSimR qSIP_confuseMtx \
--libs 2,4,6 \
BD-shift_stats.txt \
OTU_abs{abs}_PCR_sub_qSIP_atom.txt
SIPSimR heavy_confuseMtx \
--libs 2,4,6 \
BD-shift_stats.txt \
OTU_abs{abs}_PCR_sub.txt
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!chmod 777 $bashFileTmp
!cd $workDir; \
nestrun --template-file $bashFileTmp -d $buildDir --log-file cMtx.log -j 10
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def agg_cMtx(prefix):
# all data
!nestagg delim \
-d $buildDir \
-k percIncorp,percTaxa,rep \
-o $prefix-cMtx_data.txt \
--tab \
$prefix-cMtx_data.txt
# overall
!nestagg delim \
-d $buildDir \
-k percIncorp,percTaxa,rep \
-o $prefix-cMtx_overall.txt \
--tab \
$prefix-cMtx_overall.txt
# by class
!nestagg delim \
-d $buildDir \
-k percIncorp,percTaxa,rep \
-o $prefix-cMtx_byClass.txt \
--tab \
$prefix-cMtx_byClass.txt
agg_cMtx('DESeq2')
agg_cMtx('qSIP')
agg_cMtx('heavy')
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%pushnote atomIncorp_taxaIncorp complete!
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F = os.path.join(buildDir, '*-cMtx_byClass.txt')
files = glob.glob(F)
files
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%%R -i files
df_byClass = list()
for (f in files){
ff = strsplit(f, '/') %>% unlist
fff = ff[length(ff)]
df_byClass[[fff]] = read.delim(f, sep='\t')
}
df_byClass = do.call(rbind, df_byClass)
df_byClass$file = gsub('\\.[0-9]+$', '', rownames(df_byClass))
df_byClass$method = gsub('-.+', '', df_byClass$file)
rownames(df_byClass) = 1:nrow(df_byClass)
df_byClass %>% head(n=3)
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%%R -w 800 -h 550
# summarize by SIPSim rep & library rep
df_byClass.s = df_byClass %>%
group_by(method, percIncorp, percTaxa, variables) %>%
summarize(mean_value = mean(values),
sd_value = sd(values))
# plotting
ggplot(df_byClass.s, aes(variables, mean_value, color=method,
ymin=mean_value-sd_value,
ymax=mean_value+sd_value)) +
geom_pointrange(alpha=0.8) +
labs(y='Value') +
facet_grid(percIncorp ~ percTaxa) +
theme_bw() +
theme(
text = element_text(size=16),
axis.title.x = element_blank(),
axis.text.x = element_text(angle=45, hjust=1)
)
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