28 lines
861 B
Bash
Executable File
28 lines
861 B
Bash
Executable File
#! /bin/bash
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set -e
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SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
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IDENTITY=${IDENTITY:-0.99}
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THREADS=${THREADS:-6}S
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if [ "$#" -ne 3 ]; then
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echo "Usage: $0 <input_dir> <output_dir> <extension>"
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echo "Reduce redundancy of CDS files using cd-hit-est"
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exit 1
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fi
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indir=$1
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outdir=$2
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ext=$3
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mkdir -p "$outdir"
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# Process each file in the input directory with the specified extension
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for cds in "$indir"/*."$ext"; do
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stem=$(basename "$cds" ."$ext")
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echo "Processing $cds($stem) ..."
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echo "cd-hit-est -i $cds -o $outdir/$stem.cds_rr.fa -c $IDENTITY -n 10 -r 0 -T $THREADS"
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cd-hit-est -i "$cds" -o "$outdir/$stem".cds_rr.fa -c "$IDENTITY" -n 10 -r 0 -T "$THREADS"
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echo "seqkit translate $outdir/$stem.cds_rr.fa > $outdir/$stem.prot_rr.fa"
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seqkit translate "$outdir/$stem".cds_rr.fa >"$outdir/$stem".prot_rr.fa
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echo "Done."
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done
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