From e55ea2933fa19db531878b9c1c2982786a20e963 Mon Sep 17 00:00:00 2001
From: victor5lm <victor_lopez_5@hotmail.com>
Date: Mon, 9 Sep 2024 11:28:20 +0200
Subject: [PATCH] Created MLVA template as part of characterization

---
 .../05-mlva/lablog                            | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/05-mlva/lablog

diff --git a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/05-mlva/lablog b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/05-mlva/lablog
new file mode 100644
index 00000000..fb6159b6
--- /dev/null
+++ b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/05-mlva/lablog
@@ -0,0 +1,23 @@
+# micromamba activate buisciii-tools_2.1.0
+
+mkdir logs
+mkdir assemblies
+mkdir MLVA_output
+scratch_dir=$(pwd | sed 's|/data/bi/scratch_tmp|/scratch|g')
+cp ../../*_ASSEMBLY/03-assembly/unicycler/*.fasta* assemblies/
+gzip -d assemblies/*.fasta.gz
+available_primers=$(ls /data/bi/references/MLVA/*primer* | rev | cut -d "/" -f1 | rev | cut -d "_" -f1)
+
+echo "Available primers:"
+select primer in $available_primers; do
+    if [ -n "$primer" ]; then
+        echo "You selected: $primer"
+        break
+    else
+        echo "Invalid selection. Please try again."
+    fi
+done
+
+primer_file=$(ls /data/bi/references/MLVA/${primer}*)
+
+echo "srun --partition short_idx --chdir ${scratch_dir} --output logs/MLVA.log --job-name MLVA python /data/bi/pipelines/mlva/MLVA_finder.py -c -i assemblies -o MLVA_output -p ${primer_file} --full-locus-name --predicted-PCR-size-table --flanking-seq 20 &"  > _01_mlva.sh