2021-02-26 02:59:22 +01:00
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#!/bin/sh
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usage() {
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2021-02-28 02:23:58 +01:00
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echo "usage: generation.sh <number of sequences> <sequencing runs>"
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2021-02-26 02:59:22 +01:00
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exit 1
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}
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2021-02-28 02:23:58 +01:00
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if [ $# != 2 ]; then
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2021-02-26 02:59:22 +01:00
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usage
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fi
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sequences=$1
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2021-02-28 02:23:58 +01:00
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sequencing_runs=$2
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2021-03-02 20:07:05 +01:00
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read_mean_size=350
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read_variance_size=0.0
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2021-02-26 02:59:22 +01:00
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data_directory="data/"
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2021-03-10 12:33:25 +01:00
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fasta=".fasta"
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fastq=".fastq"
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filename="sequence"
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2021-02-26 02:59:22 +01:00
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prefix="curesim_"
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2021-02-28 02:23:58 +01:00
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Rscript src/repertoire.r "$sequences" "$sequencing_runs"
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2021-03-29 20:30:16 +02:00
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java -jar tools/CuReSim.jar -n "$sequencing_runs" -m "$read_mean_size" -sd "$read_variance_size" -f "$data_directory$filename$fasta" -o "$data_directory$prefix$filename$fastq"
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2021-03-11 21:28:58 +01:00
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rm "$data_directory/log.txt"
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