25 lines
698 B
Bash
Executable File
25 lines
698 B
Bash
Executable File
#! /bin/bash
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set -e
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THREADS=${THREADS:-12}
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EXT=${EXT:-"fa"}
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if [ "$#" -ne 2 ]; then
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echo "Usage: $0 <ogs_dir> <out_dir>"
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echo "Perform MACSE alignment for each orthologous group"
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exit 1
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fi
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ogs_dir=$(readlink -f "$1")
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out_dir=$2
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mkdir -p "$out_dir"
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echo "Starting MACSE alignment of orthologous groups..."
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echo -n >macse.cmds
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for og_fasta in "$ogs_dir"/*."$EXT"; do
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og_name=$(basename "$og_fasta" ."$EXT")
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out_stem="$out_dir/$og_name"
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echo "macse -prog alignSequences -seq $og_fasta -out_AA ${out_stem}.pal -out_NT ${out_stem}.nal > ${out_stem}.log 2>&1" >>macse.cmds
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done
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xargs -t -P "$THREADS" -I cmd -a macse.cmds bash -c "cmd" &&
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echo "MACSE alignment completed."
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