From bed49d5d3f5265dada04ecca01e6a3518fc6c292 Mon Sep 17 00:00:00 2001
From: Tobias Baril <46785187+TobyBaril@users.noreply.github.com>
Date: Fri, 2 Feb 2024 07:57:10 +0100
Subject: [PATCH] Update TEstrainer_for_earlGrey.sh

---
 scripts/TEstrainer/TEstrainer_for_earlGrey.sh | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/scripts/TEstrainer/TEstrainer_for_earlGrey.sh b/scripts/TEstrainer/TEstrainer_for_earlGrey.sh
index 85547d2..7139e64 100644
--- a/scripts/TEstrainer/TEstrainer_for_earlGrey.sh
+++ b/scripts/TEstrainer/TEstrainer_for_earlGrey.sh
@@ -7,13 +7,14 @@ STRAIN_SCRIPTS=INSERT_FILENAME_HERE
 FLANK=1000
 THREADS=4
 RUNS=10
+NO_SEQ=20
 # for potential folder name
 TIME=$(date +"%s")
 TIME=${TIME: -4}
 MEM_FREE="200M"
 
 # parsing
-while getopts l:g:t:f:r:d:h:M flag; do
+while getopts l:g:t:f:r:d:h:n:M flag; do
   case "${flag}" in
     l) RM_LIBRARY_PATH=${OPTARG};;
     g) GENOME=${OPTARG};;
@@ -21,6 +22,7 @@ while getopts l:g:t:f:r:d:h:M flag; do
     f) FLANK=${OPTARG};;
     r) RUNS=${OPTARG};;
     d) DATA_DIR=${OPTARG};;
+    n) NO_SEQ=${OPTARG};;
     M) MEM_FREE=${OPTARG};;
     h | *)
       print_usage
@@ -93,7 +95,7 @@ do
   parallel --bar --jobs ${THREADS} --memfree ${MEM_FREE} -a ${DATA_DIR}/run_${RUN_NO}/raw/${RM_LIBRARY}_split.txt trf ${DATA_DIR}/run_${RUN_NO}/raw/{} 2 7 7 80 10 50 500 -d -h -ngs ">" ${DATA_DIR}/run_${RUN_NO}/raw/{}.trf
   echo "Initial blast and preparation for MSA "${RUN_NO}
   # initial blast and extention
-  parallel --bar --jobs ${THREADS} --memfree ${MEM_FREE} -a ${DATA_DIR}/run_${RUN_NO}/raw/${RM_LIBRARY}_split.txt python3 ${STRAIN_SCRIPTS}/initial_mafft_setup.py -d ${DATA_DIR} -r ${RUN_NO} -s {} -g ${GENOME} -f ${FLANK} -D
+  parallel --bar --jobs ${THREADS} --memfree ${MEM_FREE} -a ${DATA_DIR}/run_${RUN_NO}/raw/${RM_LIBRARY}_split.txt python3 ${STRAIN_SCRIPTS}/initial_mafft_setup.py -d ${DATA_DIR} -r ${RUN_NO} -s {} -g ${GENOME} -f ${FLANK} -D -n ${NO_SEQ}
   
   ## first mafft alignment
   find ${DATA_DIR}/run_${RUN_NO}/to_align -type f | sed 's/.*\///' > ${DATA_DIR}/run_${RUN_NO}/to_align.txt