19 lines
520 B
Bash
Executable File
19 lines
520 B
Bash
Executable File
#! /usr/bin/env bash
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if [ "$#" -ne 3 ]; then
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echo "Usage: $0 <input_fasta_dir> <extension> <output_nexus_dir>"
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exit 1
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fi
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input_dir=$1
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extension=$2
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output_dir=$3
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mkdir -p "${output_dir}"
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for f in "${input_dir}"/*."${extension}"; do
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filename=$(basename -- "${f}")
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filename_noext="${filename%.*}"
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output_file="${output_dir}/${filename_noext}.nex"
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echo "Converting ${f} to ${output_file}"
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seqmagick convert --output-format nexus --alphabet dna --input-format fasta "${f}" "${output_file}"
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done
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