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run.sh
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run.sh
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#!/bin/bash
echo "Ex1.py"
python3 src/ex1.py
echo "Test"
python3 tests/tests.py
echo "Running commands for Exercise 2: "
echo "Please make sure that STAR was run in the bioinformatics main folder"
echo "How many alignments were reported?"
grep -v "@" Aligned.out.sam | wc -l
echo "How many reads were uniquely mapped?"
grep NH:i:1 Aligned.out.sam | wc -l
echo "How many reads were mapped to multiple loci?"
grep NH:i:2 Aligned.out.sam | wc -l
echo "+"
grep NH:i:3 Aligned.out.sam | wc -l
echo "+"
grep NH:i:4 Aligned.out.sam | wc -l
echo "How many reads could not be mapped?"
grep NH:i:0 Aligned.out.sam | wc -l
echo "Exercise 3: FASTA/FASTQ files have been created "
cat Aligned.out.sam | grep -v ^@ | awk 'NR%2==1 {print "@"$1"\n"$10"\n+\n"$11}' > Aligned.out.fastq