Description:

Simulating bacterial communities using all of the bacterial genomes available.

Workflow:

symlink all genomes
index all genomes

Setting variables



In [14]:

    
workDir = '/home/nick/notebook/SIPSim/dev/bac_genome3/'
SIPSimExe = '/home/nick/notebook/SIPSim/SIPSim'
genomeDir = '/home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/'
#genomeTable = '/var/seq_data/ncbi_db/genome/prok-bac_filt_rand.txt'

Init



In [2]:

    
import os,sys
import numpy as np
import pandas as pd
from ggplot import *
import matplotlib.pyplot as plt



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%load_ext rpy2.ipython
%matplotlib inline



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%%R
library(ggplot2)
library(dplyr)
library(tidyr)
library(gridExtra)









    





Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Loading required package: grid



In [15]:

    
if not os.path.isdir(workDir):
    os.mkdir(workDir)



In [16]:

    
workDirGenome = os.path.join(workDir, 'genomes')
if not os.path.isdir(workDirGenome):
    os.mkdir(workDirGenome)

Selecting genomes based on GC

need a example of low, mid, & high GC genomes

Calc genome GC for all genomes in dataset



In [11]:

    
%%bash -s "$genomeDir"

cd $1

find . -name "*fasta" | \
    perl -pe 's/\.fasta//' | \
    xargs -P 24 -I % bash -c \
    "seq_tools GC_content < %.fasta > %_GC.txt"



In [12]:

    
%%bash -s "$genomeDir"

cd $1

cat ./Clostridium_ljungdahlii_DSM_13528_GC.txt
cat ./Escherichia_coli_1303_GC.txt
cat ./Streptomyces_pratensis_ATCC_33331_GC.txt









    



CP001666_Clostridium_ljungdahlii_DSM_13528	4630065	31.1059347978916
CP009166_Escherichia_coli_1303	4948797	50.7275000368777
CP002475_Streptomyces_pratensis_ATCC_33331	7337497	71.1423118810134

Copying genomes



In [18]:

    
%%bash -s "$genomeDir" "$workDirGenome"

cp $1/Clostridium_ljungdahlii_DSM_13528.fasta $2
cp $1/Escherichia_coli_1303.fasta $2
cp $1/Streptomyces_pratensis_ATCC_33331.fasta $2

Indexing genomes

Needed for in-silico PCR



In [25]:

    
!cd $workDirGenome; \
printf "Clostridium_ljungdahlii_DSM_13528 Clostridium_ljungdahlii_DSM_13528.fasta\n\
Escherichia_coli_1303 Escherichia_coli_1303.fasta\n\
Streptomyces_pratensis_ATCC_33331 Streptomyces_pratensis_ATCC_33331.fasta" > genome_index.txt

!cd $workDirGenome; \
    perl -pi -e 's/ /\t/' genome_index.txt



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!cd $workDir; \
    $SIPSimExe genome_index genomes/genome_index.txt \
    --fp ./genomes/ --np 30 > genomes/index_log.txt









    



Indexing: "Clostridium_ljungdahlii_DSM_13528"
Indexing: "Escherichia_coli_1303"
Indexing: "Streptomyces_pratensis_ATCC_33331"



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