locigenesis/generation.sh

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#!/bin/sh
usage() {
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echo "usage: generation.sh <number of sequences> <sequencing runs>"
exit 1
}
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if [ $# != 2 ]; then
usage
fi
sequences=$1
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sequencing_runs=$2
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read_mean_size=350
read_variance_size=0.0
data_directory="data/"
fasta=".fasta"
fastq=".fastq"
filename="sequence"
prefix="curesim_"
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Rscript src/repertoire.r "$sequences" "$sequencing_runs"
java -jar tools/CuReSim.jar -m "$read_mean_size" -sd "$read_variance_size" -f "$data_directory$filename$fasta" -o "$data_directory$prefix$filename$fastq"