Initial commit

skills/phylo_from_buscos/scripts/generate_qc_report.sh

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+#!/bin/bash
+# Quality control report generator for compleasm results
+#
+# Usage: bash generate_qc_report.sh [output_file.csv]
+#
+# Author: Bruno de Medeiros (Field Museum)
+# Based on tutorials by Paul Frandsen (BYU)
+
+OUTPUT_FILE="${1:-qc_report.csv}"
+
+echo "Genome,Complete_SCO,Fragmented,Duplicated,Missing,Completeness(%)" > "${OUTPUT_FILE}"
+
+count=0
+for dir in 01_busco_results/*_compleasm; do
+  if [ ! -d "${dir}" ]; then
+    continue
+  fi
+
+  genome=$(basename "${dir}" _compleasm)
+  summary="${dir}/summary.txt"
+
+  if [ -f "${summary}" ]; then
+    # Parse completeness statistics from compleasm format
+    # compleasm uses: S: (single-copy), D: (duplicated), F: (fragmented), M: (missing)
+    # Format: "S:80.93%, 2283" where we need the count (2283)
+    complete=$(grep "^S:" "${summary}" | awk -F',' '{print $2}' | tr -d ' ')
+    duplicated=$(grep "^D:" "${summary}" | awk -F',' '{print $2}' | tr -d ' ')
+    fragmented=$(grep "^F:" "${summary}" | awk -F',' '{print $2}' | tr -d ' ')
+    missing=$(grep "^M:" "${summary}" | awk -F',' '{print $2}' | tr -d ' ')
+
+    # Check if all values were successfully extracted
+    if [ -z "${complete}" ] || [ -z "${fragmented}" ] || [ -z "${missing}" ]; then
+      echo "Warning: Could not parse statistics for ${genome}" >&2
+      continue
+    fi
+
+    # Calculate completeness percentage (Complete / Total * 100)
+    total=$((complete + duplicated + fragmented + missing))
+    if command -v bc &> /dev/null; then
+      completeness=$(echo "scale=2; (${complete} + ${duplicated}) / ${total} * 100" | bc)
+    else
+      # Fallback if bc not available
+      completeness=$(awk "BEGIN {printf \"%.2f\", (${complete} + ${duplicated}) / ${total} * 100}")
+    fi
+
+    echo "${genome},${complete},${fragmented},${duplicated},${missing},${completeness}" >> "${OUTPUT_FILE}"
+    count=$((count + 1))
+  else
+    echo "Warning: Summary file not found for ${genome}" >&2
+  fi
+done
+
+if [ ${count} -eq 0 ]; then
+  echo "Error: No compleasm output directories found (*_compleasm)" >&2
+  exit 1
+fi
+
+echo "QC report generated: ${OUTPUT_FILE}"
+echo "Genomes analyzed: ${count}"