Merge pull request #85 from TobyBaril/reviewer-patch-1

Update TEstrainer_for_earlGrey.sh
TobyBaril · Feb 6, 2024 · 2075115 · 2075115
2 parents cd1d16a + d8116a7
commit 2075115
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Showing 2 changed files with 14 additions and 4 deletions.
diff --git a/earlGrey b/earlGrey
@@ -18,6 +18,7 @@ usage()
 		-c == Cluster TE library to reduce redundancy? (yes/no, Default: no)
 		-m == Remove putative spurious TE annotations <100bp? (yes/no, Default: no)
 		-d == Create soft-masked genome at the end? (yes/no, Default: no)
+		-n == Max number of sequences used to generate consensus sequences (Default: 20)
 		-h == Show help
 
 	Example Usage:
@@ -159,7 +160,7 @@ deNovo1()
 strainer()
 {
 	cd ${OUTDIR}/${species}_strainer/
-	${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh -g $genome -l ${OUTDIR}/${species}_Database/${species}-families.fa -t ${ProcNum} -f $Flank -r $num
+	${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh -g $genome -l ${OUTDIR}/${species}_Database/${species}-families.fa -t ${ProcNum} -f $Flank -r $num -n $no_seq
 	latestFile="$(realpath $(ls -td -- ${OUTDIR}/${species}_strainer/*/ | head -n 1))/${species}-families.fa.strained"
 	cp $latestFile ${OUTDIR}/${species}_strainer/
 }
@@ -303,6 +304,12 @@ Checks()
 	else
 		echo "De Novo Sequences Will Be Extended Through a Maximum of $num Iterations"
 	fi
+
+	if [ -z "$no_seq" ] ; then
+		no_seq=20; echo "$no_seq sequences will be used in BEAT consensus generation"
+	else
+		echo "$no_seq sequences will be used in BEAT consensus generation"
+	fi
 
 	if [ -z "$cluster" ] || [ "$cluster" == "no" ] ; then
 		cluster=no; echo "TE library consensus sequences will not be clustered"
@@ -373,7 +380,7 @@ Checks()
 
 # Main #
 
-while getopts g:s:o:t:f:i:r:c:l:m:d:h option
+while getopts g:s:o:t:f:i:r:c:l:m:d:n:h option
 do
 	case "${option}" 
 		in
@@ -388,6 +395,7 @@ do
 		c) cluster=${OPTARG};;
 		m) margin=${OPTARG};;
 		d) softMask=${OPTARG};;
+		n) no_seq=${OPTARG};;
 		h) usage; exit 0;; 
 	esac
 done

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