35 lines
1.0 KiB
Bash
Executable File
35 lines
1.0 KiB
Bash
Executable File
#! /bin/bash
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set -e
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SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
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THREADS=${THREADS:-12}
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if [ "$#" -ne 5 ]; then
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echo "Usage: $0 <ogs_dir> <hmmsearch_result_dir> <all_cds.fa> <output_dir> <homolog_stem>"
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echo "Integrate hmmsearch results to new orthologous groups directory and perform MACSE alignment"
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exit 1
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fi
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ogs_dir=$(readlink -f "$1")
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search_dir=$(readlink -f "$2")
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all_cds=$(readlink -f "$3")
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out_dir=$4
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stem=$5
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echo "Integrating hmmsearch results to new orthologous groups directory..."
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python3 "$SCRIPTS"/miscs/hmmsearch_result_to_new_ogs_dir.py \
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-d "$ogs_dir" \
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-t "$search_dir" \
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-f "$all_cds" \
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-o "$out_dir" \
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-s "$stem"
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echo "Integration completed."
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echo "Starting MACSE alignment of orthologous groups..."
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echo -n >macse.cmds
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for og_dir in "$out_dir"/ogs/*; do
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j=$(basename "$og_dir")
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echo "cd $og_dir && bash $SCRIPTS/miscs/macse.sh ${j}_${stem}.fa ${j}.fa $j" >>macse.cmds
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done
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xargs -t -P "$THREADS" -I cmd -a macse.cmds bash -c "cmd"
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echo "MACSE alignment completed."
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