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Fix CRLF line endings in shell scripts
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‎run-analysis-cs.sh‎

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#!/bin/bash
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# DNA Barcoding Analysis - Simple Workflow (Codespaces Version)
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# Copy your .ab1 files to data/student_sequences/ then run this script
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set -e
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# Suppress Python deprecation warnings (BioPython pairwise2)
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export PYTHONWARNINGS="ignore::DeprecationWarning"
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OUTPUT_DIR="results/my_analysis"
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# Create output directories automatically
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mkdir -p results/my_analysis/{01_qc,02_consensus,03_alignment,04_phylogeny,05_blast}
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mkdir -p results/lab_analysis
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# Start logging
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LOG_FILE="results/my_analysis/student.log"
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exec > >(tee "$LOG_FILE") 2>&1
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echo "=== Student Analysis Pipeline Started ==="
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echo "☁️ Environment: GitHub Codespaces"
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echo "📝 Log file: $LOG_FILE"
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echo ""
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# Show beautiful welcome banner using Rich
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python3 modules/show_welcome.py --welcome --mode analysis
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echo ""
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echo "REQUIREMENTS:"
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echo " 1. Your .ab1 files must be in: data/student_sequences/"
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echo " 2. You must have completed the tutorial first: ./tutorial-cs.sh"
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echo ""
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echo "Starting analysis..."
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# Show Step 1 banner
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python3 modules/show_welcome.py --step 1
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python3 modules/01_quality_control/qc_chromatograms.py \
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data/student_sequences/ \
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$OUTPUT_DIR/01_qc/
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echo "✓ Step 1 complete!"
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# Show Step 2 banner
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python3 modules/show_welcome.py --step 2
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python3 -W ignore::DeprecationWarning modules/02_consensus/create_consensus.py \
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$OUTPUT_DIR/01_qc/passed_sequences.fasta \
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$OUTPUT_DIR/02_consensus/ \
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--pairs-only 2>&1 | grep -v "BiopythonDeprecationWarning\|Bio.pairwise2\|warnings.warn"
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echo "✓ Step 2 complete!"
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# Show Step 3 banner
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python3 modules/show_welcome.py --step 3
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cat $OUTPUT_DIR/02_consensus/consensus_sequences.fasta \
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data/reference_sequences/socal_mosquitoes.fasta \
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> $OUTPUT_DIR/02_consensus/combined_with_references.fasta
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NUM_SEQS=$(grep -c "^>" $OUTPUT_DIR/02_consensus/combined_with_references.fasta)
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echo "Combined $NUM_SEQS sequences (your samples + references)"
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echo "✓ Step 3 complete!"
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# Show Step 4 banner
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python3 modules/show_welcome.py --step 4
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echo ""
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# Alignment
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python3 modules/03_alignment/align_sequences.py \
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$OUTPUT_DIR/02_consensus/combined_with_references.fasta \
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$OUTPUT_DIR/03_alignment/
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echo ""
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# Tree
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python3 modules/04_phylogeny/build_tree.py \
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$OUTPUT_DIR/03_alignment/aligned_sequences.fasta \
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$OUTPUT_DIR/04_phylogeny/
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echo "✓ Step 4 complete!"
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# Show Step 5 banner
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python3 modules/show_welcome.py --step 5
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python3 modules/05_identification/identify_species.py \
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$OUTPUT_DIR/02_consensus/consensus_sequences.fasta \
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$OUTPUT_DIR/05_blast/
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echo "✓ Step 5 complete!"
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# Show Step 6 banner
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python3 modules/show_welcome.py --step 6
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echo "Generating lab analysis report (extraction, PCR, sequencing results)..."
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echo ""
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cd modules/06_lab_data_analysis
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python3 plot_extraction.py && \
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python3 plot_quality.py && \
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python3 plot_pcr.py && \
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python3 plot_sequencing.py && \
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python3 plot_teams.py && \
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python3 generate_report.py
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cd ../..
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echo "✓ Step 6 complete!"
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# Show completion banner using Rich
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python3 modules/show_welcome.py --complete
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echo ""
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echo "Your results are in: $OUTPUT_DIR/"
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echo ""
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echo " 01_qc/ - Quality control report"
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echo " 02_consensus/ - Consensus sequences"
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echo " 03_alignment/ - Sequence alignment"
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echo " 04_phylogeny/ - Phylogenetic tree"
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echo " 05_blast/ - Species identification"
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echo ""
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echo "Lab analysis report: results/lab_analysis/"
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echo ""
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echo "Open these files:"
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echo " • $OUTPUT_DIR/01_qc/qc_report.html"
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echo " • $OUTPUT_DIR/04_phylogeny/tree.png"
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echo " • $OUTPUT_DIR/05_blast/identification_report.html"
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echo " • results/lab_analysis/lab_report.html"
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echo ""
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echo "=== Student Analysis Pipeline Completed ==="
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# Clean ANSI color codes from log file for readability in text editors
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sed 's/\x1b\[[0-9;]*m//g' "$LOG_FILE" > "${LOG_FILE}.clean" && mv "${LOG_FILE}.clean" "$LOG_FILE"
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echo "Log saved to: $LOG_FILE"
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#!/bin/bash
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# DNA Barcoding Analysis - Simple Workflow (Codespaces Version)
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# Copy your .ab1 files to data/student_sequences/ then run this script
4+
5+
set -e
6+
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# Suppress Python deprecation warnings (BioPython pairwise2)
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export PYTHONWARNINGS="ignore::DeprecationWarning"
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OUTPUT_DIR="results/my_analysis"
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# Create output directories automatically
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mkdir -p results/my_analysis/{01_qc,02_consensus,03_alignment,04_phylogeny,05_blast}
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mkdir -p results/lab_analysis
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# Start logging
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LOG_FILE="results/my_analysis/student.log"
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exec > >(tee "$LOG_FILE") 2>&1
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echo "=== Student Analysis Pipeline Started ==="
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echo "☁️ Environment: GitHub Codespaces"
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echo "📝 Log file: $LOG_FILE"
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echo ""
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# Show beautiful welcome banner using Rich
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python3 modules/show_welcome.py --welcome --mode analysis
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echo ""
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echo "REQUIREMENTS:"
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echo " 1. Your .ab1 files must be in: data/student_sequences/"
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echo " 2. You must have completed the tutorial first: ./tutorial-cs.sh"
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echo ""
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echo "Starting analysis..."
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# Show Step 1 banner
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python3 modules/show_welcome.py --step 1
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python3 modules/01_quality_control/qc_chromatograms.py \
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data/student_sequences/ \
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$OUTPUT_DIR/01_qc/
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echo "✓ Step 1 complete!"
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# Show Step 2 banner
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python3 modules/show_welcome.py --step 2
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python3 -W ignore::DeprecationWarning modules/02_consensus/create_consensus.py \
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$OUTPUT_DIR/01_qc/passed_sequences.fasta \
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$OUTPUT_DIR/02_consensus/ \
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--pairs-only 2>&1 | grep -v "BiopythonDeprecationWarning\|Bio.pairwise2\|warnings.warn"
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echo "✓ Step 2 complete!"
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# Show Step 3 banner
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python3 modules/show_welcome.py --step 3
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cat $OUTPUT_DIR/02_consensus/consensus_sequences.fasta \
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data/reference_sequences/socal_mosquitoes.fasta \
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> $OUTPUT_DIR/02_consensus/combined_with_references.fasta
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NUM_SEQS=$(grep -c "^>" $OUTPUT_DIR/02_consensus/combined_with_references.fasta)
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echo "Combined $NUM_SEQS sequences (your samples + references)"
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echo "✓ Step 3 complete!"
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# Show Step 4 banner
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python3 modules/show_welcome.py --step 4
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echo ""
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# Alignment
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python3 modules/03_alignment/align_sequences.py \
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$OUTPUT_DIR/02_consensus/combined_with_references.fasta \
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$OUTPUT_DIR/03_alignment/
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echo ""
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# Tree
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python3 modules/04_phylogeny/build_tree.py \
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$OUTPUT_DIR/03_alignment/aligned_sequences.fasta \
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$OUTPUT_DIR/04_phylogeny/
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echo "✓ Step 4 complete!"
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# Show Step 5 banner
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python3 modules/show_welcome.py --step 5
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python3 modules/05_identification/identify_species.py \
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$OUTPUT_DIR/02_consensus/consensus_sequences.fasta \
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$OUTPUT_DIR/05_blast/
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echo "✓ Step 5 complete!"
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# Show Step 6 banner
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python3 modules/show_welcome.py --step 6
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echo "Generating lab analysis report (extraction, PCR, sequencing results)..."
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echo ""
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cd modules/06_lab_data_analysis
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python3 plot_extraction.py && \
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python3 plot_quality.py && \
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python3 plot_pcr.py && \
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python3 plot_sequencing.py && \
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python3 plot_teams.py && \
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python3 generate_report.py
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cd ../..
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echo "✓ Step 6 complete!"
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# Show completion banner using Rich
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python3 modules/show_welcome.py --complete
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echo ""
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echo "Your results are in: $OUTPUT_DIR/"
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echo ""
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echo " 01_qc/ - Quality control report"
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echo " 02_consensus/ - Consensus sequences"
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echo " 03_alignment/ - Sequence alignment"
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echo " 04_phylogeny/ - Phylogenetic tree"
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echo " 05_blast/ - Species identification"
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echo ""
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echo "Lab analysis report: results/lab_analysis/"
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echo ""
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echo "Open these files:"
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echo " • $OUTPUT_DIR/01_qc/qc_report.html"
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echo " • $OUTPUT_DIR/04_phylogeny/tree.png"
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echo " • $OUTPUT_DIR/05_blast/identification_report.html"
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echo " • results/lab_analysis/lab_report.html"
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echo ""
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echo "=== Student Analysis Pipeline Completed ==="
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# Clean ANSI color codes from log file for readability in text editors
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sed 's/\x1b\[[0-9;]*m//g' "$LOG_FILE" > "${LOG_FILE}.clean" && mv "${LOG_FILE}.clean" "$LOG_FILE"
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echo "Log saved to: $LOG_FILE"

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