Initial commit
This commit is contained in:
Zhongwei Li
247
skills/phylo_from_buscos/scripts/run_alicut.sh
Executable file
247
skills/phylo_from_buscos/scripts/run_alicut.sh
Executable file
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#!/bin/bash
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# run_alicut.sh
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# Wrapper script for running ALICUT to remove Aliscore-identified RSS positions
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# Removes randomly similar sequence sections from alignments
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#
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# Usage:
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# bash run_alicut.sh [aliscore_dir] [options]
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#
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# Options:
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# -r Remain stem positions (for RNA secondary structures)
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# -c Remove codon (translate AA positions to nucleotide triplets)
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# -3 Remove only 3rd codon positions
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# -s Silent mode (non-interactive, use defaults)
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#
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# Requirements:
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# - ALICUT_V2.31.pl in PATH or same directory
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# - Perl with File::Copy, Tie::File, Term::Cap modules
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# - Aliscore output directory with *_List_*.txt and original .fas file
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set -euo pipefail
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# Script directory
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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# Check for ALICUT script
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if command -v ALICUT_V2.31.pl &> /dev/null; then
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ALICUT_SCRIPT="ALICUT_V2.31.pl"
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elif [ -f "${SCRIPT_DIR}/ALICUT_V2.31.pl" ]; then
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ALICUT_SCRIPT="${SCRIPT_DIR}/ALICUT_V2.31.pl"
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elif [ -f "./ALICUT_V2.31.pl" ]; then
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ALICUT_SCRIPT="./ALICUT_V2.31.pl"
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else
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echo "ERROR: ALICUT_V2.31.pl not found in PATH, script directory, or current directory"
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echo "Please download from: https://www.zfmk.de/en/research/research-centres-and-groups/alicut"
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exit 1
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fi
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# Function to display usage
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usage() {
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cat <<EOF
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Usage: $0 [aliscore_dir] [options]
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Run ALICUT to remove Aliscore-identified randomly similar sequence sections.
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Arguments:
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aliscore_dir Directory containing Aliscore output files
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Options:
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-r Remain stem positions in RNA secondary structure alignments
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-c Remove entire codon (translates AA RSS positions to nt triplets)
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-3 Remove only 3rd codon position of identified RSS
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-s Silent/scripted mode (non-interactive, use defaults)
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-h Display this help message
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Input Requirements:
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The aliscore_dir must contain:
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- Original FASTA alignment file (*.fas)
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- Aliscore List file (*_List_random.txt or *_List_*.txt)
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Examples:
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# Basic usage (interactive mode)
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bash run_alicut.sh aliscore_alignment1
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# Silent mode with defaults
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bash run_alicut.sh aliscore_alignment1 -s
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# Remain RNA stem positions
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bash run_alicut.sh aliscore_16S -r -s
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# Remove entire codons (for back-translation)
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bash run_alicut.sh aliscore_protein1 -c -s
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# Process all Aliscore output directories
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for dir in aliscore_*/; do
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bash run_alicut.sh "\${dir}" -s
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done
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Output Files (in aliscore_dir):
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- ALICUT_[alignment].fas : Trimmed alignment
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- ALICUT_info.xls : Statistics (taxa, positions removed, etc.)
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- ALICUT_Struc_info_*.txt : Structure information (if RNA detected)
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Citation:
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Kück P, Meusemann K, Dambach J, Thormann B, von Reumont BM, Wägele JW,
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Misof B (2010) Parametric and non-parametric masking of randomness in
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sequence alignments can be improved and leads to better resolved trees.
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Front Zool 7:10. doi: 10.1186/1742-9994-7-10
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EOF
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exit 0
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}
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# Parse command line arguments
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ALISCORE_DIR=""
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ALICUT_OPTS=""
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SILENT_MODE=false
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if [ $# -eq 0 ]; then
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usage
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fi
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ALISCORE_DIR="$1"
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shift
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# Validate directory exists
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if [ ! -d "${ALISCORE_DIR}" ]; then
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echo "ERROR: Aliscore directory not found: ${ALISCORE_DIR}"
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exit 1
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fi
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# Parse ALICUT options
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while [ $# -gt 0 ]; do
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case "$1" in
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-h|--help)
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usage
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;;
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-r)
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ALICUT_OPTS="${ALICUT_OPTS} -r"
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shift
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;;
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-c)
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ALICUT_OPTS="${ALICUT_OPTS} -c"
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shift
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;;
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-3)
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ALICUT_OPTS="${ALICUT_OPTS} -3"
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shift
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;;
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-s|--silent)
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SILENT_MODE=true
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ALICUT_OPTS="${ALICUT_OPTS} -s"
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shift
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;;
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*)
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echo "ERROR: Unknown option: $1"
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usage
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;;
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esac
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done
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# Change to Aliscore output directory
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cd "${ALISCORE_DIR}"
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echo "Processing Aliscore output in: ${ALISCORE_DIR}"
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# Find List file
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LIST_FILE=$(ls *_List_*.txt 2>/dev/null | head -n 1)
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if [ -z "${LIST_FILE}" ]; then
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echo "ERROR: No Aliscore List file found (*_List_*.txt)"
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echo "Make sure Aliscore completed successfully"
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exit 1
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fi
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echo "Found List file: ${LIST_FILE}"
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# Find original FASTA file
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FASTA_FILE=$(find . -maxdepth 1 \( -name "*.fas" -o -name "*.fasta" \) -type f | head -n 1 | sed 's|^\./||')
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if [ -z "${FASTA_FILE}" ]; then
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echo "ERROR: No FASTA alignment file found (*.fas or *.fasta)"
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echo "ALICUT requires the original alignment file in the same directory as List file"
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exit 1
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fi
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echo "Found FASTA file: ${FASTA_FILE}"
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# Check if List file contains RSS positions
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RSS_COUNT=$(wc -w < "${LIST_FILE}" || echo "0")
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if [ "${RSS_COUNT}" -eq 0 ]; then
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echo "WARNING: List file is empty (no RSS positions identified)"
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echo "Aliscore found no randomly similar sequences to remove"
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echo "Skipping ALICUT - alignment is already clean"
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# Create a symbolic link to indicate no trimming was needed
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ln -sf "${FASTA_FILE}" "ALICUT_${FASTA_FILE}"
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echo "Created symbolic link: ALICUT_${FASTA_FILE} -> ${FASTA_FILE}"
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cd ..
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exit 0
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fi
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echo "Found ${RSS_COUNT} RSS positions to remove"
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# Run ALICUT
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echo ""
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echo "Running ALICUT..."
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echo "Options: ${ALICUT_OPTS}"
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# Construct ALICUT command
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ALICUT_CMD="perl ${ALICUT_SCRIPT} ${ALICUT_OPTS}"
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if [ "${SILENT_MODE}" = true ]; then
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echo "Command: ${ALICUT_CMD}"
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eval ${ALICUT_CMD}
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else
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echo "Running ALICUT in interactive mode..."
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echo "Press 's' and Enter to start with current options"
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echo ""
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perl "${ALICUT_SCRIPT}" ${ALICUT_OPTS}
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fi
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# Check if ALICUT completed successfully
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if [ $? -eq 0 ]; then
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echo ""
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echo "ALICUT completed successfully"
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# Find output file
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OUTPUT_FILE=$(ls ALICUT_*.fas ALICUT_*.fasta 2>/dev/null | head -n 1)
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if [ -n "${OUTPUT_FILE}" ]; then
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echo ""
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echo "Output files:"
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ls -lh ALICUT_* 2>/dev/null
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# Calculate and report trimming statistics (handle multi-line FASTA format)
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if [ -f "${OUTPUT_FILE}" ]; then
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ORIGINAL_LENGTH=$(awk '/^>/ {if (seq) {print seq; seq=""}; next} {seq = seq $0} END {if (seq) print seq}' "${FASTA_FILE}" | head -n 1 | wc -c)
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TRIMMED_LENGTH=$(awk '/^>/ {if (seq) {print seq; seq=""}; next} {seq = seq $0} END {if (seq) print seq}' "${OUTPUT_FILE}" | head -n 1 | wc -c)
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REMOVED_LENGTH=$((ORIGINAL_LENGTH - TRIMMED_LENGTH))
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PERCENT_REMOVED=$(awk "BEGIN {printf \"%.1f\", (${REMOVED_LENGTH}/${ORIGINAL_LENGTH})*100}")
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echo ""
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echo "Trimming statistics:"
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echo " Original length: ${ORIGINAL_LENGTH} bp"
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echo " Trimmed length: ${TRIMMED_LENGTH} bp"
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echo " Removed: ${REMOVED_LENGTH} bp (${PERCENT_REMOVED}%)"
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fi
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# Check for info file
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if [ -f "ALICUT_info.xls" ]; then
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echo ""
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echo "Detailed statistics in: ALICUT_info.xls"
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fi
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else
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echo "WARNING: Expected output file ALICUT_*.fas not found"
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fi
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else
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echo "ERROR: ALICUT failed"
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cd ..
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exit 1
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fi
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# Return to parent directory
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cd ..
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echo ""
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echo "Done: ${ALISCORE_DIR}"
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