agent
e467d67723
- Created `mbblock.txt` for MrBayes configuration. - Implemented `mrbayes.sh` to convert FASTA to Nexus and run MrBayes. - Developed `raxml.sh` to run modeltest-ng and raxml-ng on alignments. - Added `04.filter_ogs.sh` to filter orthologous groups based on taxon count and sequence length. - Implemented `01.run_mrbayes.sh` to execute MrBayes for multiple FASTA files. - Created `02.mbsum.sh` to summarize MrBayes output while skipping high DSF analyses. - Developed `03.run_raxml.sh` to run raxml-ng on filtered alignments.
22 lines
606 B
Bash
Executable File
22 lines
606 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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if [ "$#" -ne 3 ]; then
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echo "Usage: $0 <input_fasta_dir> <extension> <output_dir>"
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echo "Run MrBayes for each fasta file in the input directory"
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exit 1
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fi
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input_dir=$(readlink -f "$1")
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ext=$2
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output_dir=$(readlink -f "$3")
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mkdir -p "${output_dir}"
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echo -n >mrbayes.cmds
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for f in "${input_dir}"/*."${ext}"; do
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j=$(basename "$f" ."${ext}")
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echo "bash $SCRIPTS/miscs/mrbayes.sh $f ${output_dir}/${j}/${j}.nex" >>mrbayes.cmds
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done
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xargs -t -P 12 -I cmd -a mrbayes.cmds bash -c "cmd"
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echo "All MrBayes analyses are done!"
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