21 lines
530 B
Bash
Executable File
21 lines
530 B
Bash
Executable File
#! /bin/bash
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set -e
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THREADS=${THREADS:-12}
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if [ "$#" -ne 3 ]; then
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echo "Usage: $0 <nal_dir> <out_dir> <ext>"
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echo "Trim MACSE nucleotide alignments using trimal"
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exit 1
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fi
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nal_dir=$(readlink -f "$1")
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out_dir=$(readlink -f "$2")
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ext=$3
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mkdir -p "$out_dir"
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echo -n >trimal.cmds
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for i in "$nal_dir"/*."$ext"; do
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j=$(basename "$i" ."$ext")
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echo "trimal -in $i -out $out_dir/${j}.trimed.fa -automated1 -resoverlap 0.5 -seqoverlap 50" >>trimal.cmds
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done
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xargs -t -P "$THREADS" -I cmd -a trimal.cmds bash -c "cmd"
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