Update TEstrainer_for_earlGrey.sh

TobyBaril · Feb 2, 2024 · bed49d5 · bed49d5
1 parent cd1d16a
commit bed49d5
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/scripts/TEstrainer/TEstrainer_for_earlGrey.sh b/scripts/TEstrainer/TEstrainer_for_earlGrey.sh
@@ -7,20 +7,22 @@ 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=${OPTARG};;
     t) THREADS=${OPTARG};;
     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