From 3e434f8e3d851041c0eb518cc24be91e2e5ed3f1 Mon Sep 17 00:00:00 2001
From: Erik Garrison <erik.garrison@gmail.com>
Date: Sat, 1 Jun 2024 15:54:45 -0500
Subject: [PATCH] script to make test cases for wflign

---
 scripts/make_align_test_case.sh | 78 +++++++++++++++++++++++++++++++++
 1 file changed, 78 insertions(+)
 create mode 100755 scripts/make_align_test_case.sh

diff --git a/scripts/make_align_test_case.sh b/scripts/make_align_test_case.sh
new file mode 100755
index 00000000..6244595a
--- /dev/null
+++ b/scripts/make_align_test_case.sh
@@ -0,0 +1,78 @@
+#!/bin/bash
+
+# Function to display usage
+usage() {
+    echo "Usage: $0 -p <paf_file> -f <fasta_file> -o <output_prefix>"
+    echo "  -p, --paf       PAF file"
+    echo "  -f, --fasta     FASTA file"
+    echo "  -o, --output    Output prefix for the new FASTA and adjusted PAF files"
+    exit 1
+}
+
+# Parse command-line arguments
+PARSED_ARGUMENTS=$(getopt -a -n "$0" -o p:f:o: --long paf:,fasta:,output: -- "$@")
+VALID_ARGUMENTS=$?
+if [ "$VALID_ARGUMENTS" != "0" ]; then
+    usage
+fi
+
+eval set -- "$PARSED_ARGUMENTS"
+while :
+do
+    case "$1" in
+        -p | --paf) PAF_FILE="$2" ; shift 2 ;;
+        -f | --fasta) FASTA_FILE="$2" ; shift 2 ;;
+        -o | --output) OUTPUT_PREFIX="$2" ; shift 2 ;;
+        --) shift ; break ;;
+        *) usage ;;
+    esac
+done
+
+# Validate arguments
+if [ -z "$PAF_FILE" ] || [ -z "$FASTA_FILE" ] || [ -z "$OUTPUT_PREFIX" ]; then
+    usage
+fi
+
+OUTPUT_FASTA="${OUTPUT_PREFIX}.fa"
+OUTPUT_PAF="${OUTPUT_PREFIX}.paf"
+
+# Extract the first alignment from the PAF file
+read -r line < "$PAF_FILE"
+
+# Parse the alignment fields
+IFS=$'\t' read -r -a fields <<< "$line"
+
+# Extract query and target information
+query_name="${fields[0]}"
+query_start="${fields[2]}"
+query_end="${fields[3]}"
+target_name="${fields[5]}"
+target_start="${fields[7]}"
+target_end="${fields[8]}"
+
+# Extract sequences using samtools faidx
+samtools faidx "$FASTA_FILE" "$query_name:$query_start-$query_end" > "$OUTPUT_FASTA"
+samtools faidx "$FASTA_FILE" "$target_name:$target_start-$target_end" >> "$OUTPUT_FASTA"
+
+qname=$(grep ^">" "$OUTPUT_FASTA" | head -n 1 | sed 's/^>//')
+tname=$(grep ^">" "$OUTPUT_FASTA" | tail -n 1 | sed 's/^>//')
+
+# Adjust the PAF file
+awk -v qname=$qname \
+    -v tname=$tname \
+    '{
+        if (NF > 0) {
+            query_length = $4 - $3;
+            target_length = $9 - $8;
+            $1 = qname;
+            $6 = tname;
+            $2 = query_length;
+            $3 = 0;
+            $4 = query_length;
+            $7 = target_length;
+            $8 = 0;
+            $9 = target_length;
+            print $0;
+        }
+    }' "$PAF_FILE" | tr ' ' '\t' > "$OUTPUT_PAF"
+