locigenesis/generation.sh

#!/bin/sh

usage() {
	echo "usage: generation.sh <number of sequences> <number_of_reads>"
	exit 1
}

if [ $# != 2 ]; then
	usage
fi

sequences=$1
number_of_reads=$2
data_directory="data/"
fastq=".fastq"
filename="sequence"
prefix="curesim_"

Rscript src/repertoire.r "$sequences" "$number_of_reads" &&
	CuReSim -f "$data_directory$filename$fastq" -o "$data_directory$prefix$filename$fastq"
Rscript src/alignment.r
rm "$data_directory/log.txt"
Create a script that executes the pipeline 2021-02-26 02:59:22 +01:00			`#!/bin/sh`

			`usage() {`
Rename sequencing_runs to number_of_reads 2021-04-21 20:09:02 +02:00			`echo "usage: generation.sh <number of sequences> <number_of_reads>"`
Create a script that executes the pipeline 2021-02-26 02:59:22 +01:00			`exit 1`
			`}`

Add sequencing runs CLI argument 2021-02-28 02:23:58 +01:00			`if [ $# != 2 ]; then`
Create a script that executes the pipeline 2021-02-26 02:59:22 +01:00			`usage`
			`fi`

			`sequences=$1`
Rename sequencing_runs to number_of_reads 2021-04-21 20:09:02 +02:00			`number_of_reads=$2`
Create a script that executes the pipeline 2021-02-26 02:59:22 +01:00			`data_directory="data/"`
Change CuReSim output file extension to FASTQ 2021-03-10 12:33:25 +01:00			`fastq=".fastq"`
			`filename="sequence"`
Create a script that executes the pipeline 2021-02-26 02:59:22 +01:00			`prefix="curesim_"`

Generate FASTQ files from the simulated repertoire 2021-04-22 13:36:43 +02:00			`Rscript src/repertoire.r "$sequences" "$number_of_reads" &&`
Create a Nix derivation for CuReSim 2021-05-04 00:57:35 +02:00			`CuReSim -f "$data_directory$filename$fastq" -o "$data_directory$prefix$filename$fastq"`
Add alignment to generation script 2021-05-03 21:51:48 +02:00			`Rscript src/alignment.r`
Delete CuReSim log file after execution 2021-03-11 21:28:58 +01:00			`rm "$data_directory/log.txt"`