21 lines
485 B
Bash
21 lines
485 B
Bash
#! /bin/bash
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set -e
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dirname=$(dirname "$0")
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if [ "$#" -ne 2 ]; then
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echo "Usage: $0 <input_fasta> <output_nexus>"
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exit 1
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fi
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in_fasta=$(readlink -f "$1")
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out_nex=$2
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# Convert fasta to nexus
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out_dir=$(dirname "$out_nex")
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mkdir -p "$out_dir"
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seqmagick convert --output-format nexus --alphabet dna --input-format fasta "$in_fasta" "$out_nex"
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# append MrBayes block to nexus file
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cat "$dirname/mbblock.txt" >>"$out_nex"
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# Run MrBayes
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mb "$out_nex" >"${out_dir}"/mrbayes.log 2>&1
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