23 lines
463 B
Bash
Executable File
23 lines
463 B
Bash
Executable File
#!/bin/sh
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usage() {
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echo "usage: generation.sh <number of sequences> <number_of_reads>"
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exit 1
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}
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if [ $# != 2 ]; then
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usage
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fi
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sequences=$1
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number_of_reads=$2
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data_directory="data/"
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fastq=".fastq"
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filename="sequence"
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prefix="curesim_"
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Rscript src/repertoire.r "$sequences" "$number_of_reads" &&
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java -jar tools/CuReSim.jar -f "$data_directory$filename$fastq" -o "$data_directory$prefix$filename$fastq"
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Rscript src/alignment.r
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rm "$data_directory/log.txt"
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