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Change CuReSim output file extension to FASTQ

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coolneng 2021-03-10 12:33:25 +01:00
parent d2e45bc00f
commit f4a001f821
Signed by: coolneng
GPG Key ID: 9893DA236405AF57
2 changed files with 5 additions and 2 deletions
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1
.gitignore vendored
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@ -1,2 +1,3 @@
*.txt *.txt
*.fasta *.fasta
*.fastq

6
generation.sh
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@ -14,8 +14,10 @@ sequencing_runs=$2
read_mean_size=350 read_mean_size=350
read_variance_size=0.0 read_variance_size=0.0
data_directory="data/" data_directory="data/"
file="sequence.fasta" fasta=".fasta"
fastq=".fastq"
filename="sequence"
prefix="curesim_" prefix="curesim_"
Rscript src/repertoire.r "$sequences" "$sequencing_runs" Rscript src/repertoire.r "$sequences" "$sequencing_runs"
java -jar tools/CuReSim.jar -m "$read_mean_size" -sd "$read_variance_size" -f "$data_directory$file" -o "$data_directory$prefix$file" java -jar tools/CuReSim.jar -m "$read_mean_size" -sd "$read_variance_size" -f "$data_directory$filename$fasta" -o "$data_directory$prefix$filename$fastq"