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Friday, February 24, 2017

use bash associate array to generate commands

The problem

I am running pyclone recently to determine the clonality of our collected tumor samples. It needs tumor purity (estimated from sequenza) for input. I have 24 samples, and I want to generate pyclone commands for all of them.

The solution

I usually generate command by bash and then use another bash wrapper to generate pbs files on HPC ((Thanks to @SBAmin). now for each patient, I have two samples. How should I generate the commands? I am still better in R and Unix than python, so I used the associated array in bash.
First, generate a file containing the tumor purity for each tumor:
head -6 all_tumor_purity_no_header.txt
0.69    Pa25T1
0.26    Pa25T2
0.49    Pa26T1
0.37    Pa26T2
0.9 Pa27T1
0.92    Pa27T2
This bash script uses associate array to contain tumor purity. read more at
#! /bin/bash
set -euo pipefail

## build the array to contain the tumor purity, like a python dict
## have to declare by -A
declare -A cols

while read purity sample
done < all_purity_no_header.txt 

echo ${cols[@]}

## generate commands
for i in Pa{25..37}
   echo PyClone run_analysis_pipeline --in_file ${i}T1_pyclone.tsv ${i}T2_pyclone.tsv --tumour_contents ${cols[${i}T1]} ${cols[${i}T2]} --samples ${i}T1 ${i}T2 --density pyclone_binomial --working_dir ${i}T_pyclone_analysis --min_cluster_size 2 --seed 123 --num_iters 50000 > ${i}_pyclone_commands.txt
chmod u+x
what you get: cat *commands.txt
PyClone run_analysis_pipeline --in_file Pa25T1_pyclone.tsv Pa25T2_pyclone.tsv --tumour_contents 0.69 0.26 --samples Pa25T1 Pa25T2 --density pyclone_binomial --working_dir Pa25T_pyclone_analysis --min_cluster_size 2 --seed 123 --num_iters 50000
PyClone run_analysis_pipeline --in_file Pa26T1_pyclone.tsv Pa26T2_pyclone.tsv --tumour_contents 0.49 0.37 --samples Pa26T1 Pa26T2 --density pyclone_binomial --working_dir Pa26T_pyclone_analysis --min_cluster_size 2 --seed 123 --num_iters 50000
PyClone run_analysis_pipeline --in_file Pa27T1_pyclone.tsv Pa27T2_pyclone.tsv --tumour_contents 0.9 0.92 --samples Pa27T1 Pa27T2 --density pyclone_binomial --working_dir Pa27T_pyclone_analysis --min_cluster_size 2 --seed 123 --num_iters 50000
use the makemsub wrapper:

find *commands.txt | parallel 'makemsub -a {} -j {/.} -o a -c 4 -t "48:00:00" -m 16g > {/.}.pbs'

for pbs in *pbs
  msub $pbs
  sleep 1
I usually do it for simple tasks. e.g. only one or two commands are evoked. For more complex workflows, a workflow tool such as snakemake is better.

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