Merge pull request #53 from CALeDNA/develop

LCA variable
CALeDNA · Feb 6, 2024 · 01904d3 · 01904d3
2 parents e4eebd3 + 240a308
commit 01904d3
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Showing 2 changed files with 9 additions and 6 deletions.
diff --git a/crux/vars/crux_vars.sh.sample b/crux/vars/crux_vars.sh.sample
@@ -7,7 +7,9 @@ BLAST_THREADS=8
 RUNID="2023-04-07"
 BUCKET=[GET_BUCKET_NAME]
 
+# tronko-assign
 ASSIGNXL=("ITS1_Fungi")
+LCA=5
 
 # Obitools ecopcr variables
 ERROR=3

diff --git a/tronko/assign/assign.sh b/tronko/assign/assign.sh
@@ -6,6 +6,7 @@ OUTPUT="/etc/ben/output"
 PAIRED=""
 UNPAIRED_F=""
 UNPAIRED_R=""
+LCA=5
 while getopts "i:p:r:123" opt; do
     case $opt in
         i) PROJECTID="$OPTARG"
@@ -216,7 +217,7 @@ then
     fi
 
     # run tronko assign paired v1
-    time tronko-assign -r -f $PROJECTID-$PRIMER/tronkodb/reference_tree.txt.gz -a $PROJECTID-$PRIMER/tronkodb/$PRIMER.fasta -p -z -w -1 $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-paired_F.fasta -2 $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-paired_R.fasta -6 -C 1 -c 5 -o $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-paired.txt
+    time tronko-assign -r -f $PROJECTID-$PRIMER/tronkodb/reference_tree.txt.gz -a $PROJECTID-$PRIMER/tronkodb/$PRIMER.fasta -p -z -w -1 $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-paired_F.fasta -2 $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-paired_R.fasta -6 -C 1 -c $LCA -o $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-paired.txt
 
     # filter tronko output
     /mnt/chisquared_filter.pl $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-paired.txt $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-paired_F.fasta $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-paired_R.fasta $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-paired_F.asv $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-paired_R.asv
@@ -228,7 +229,7 @@ then
     fi
 
     # run tronko assign paired v2 (rc)
-    time tronko-assign -r -f $PROJECTID-$PRIMER/tronkodb/reference_tree.txt.gz -a $PROJECTID-$PRIMER/tronkodb/$PRIMER.fasta -p -z -w -1 $PROJECTID-$PRIMER-rc/$PROJECTID-$PRIMER-paired_F.fasta -2 $PROJECTID-$PRIMER-rc/$PROJECTID-$PRIMER-paired_R.fasta -6 -C 1 -c 5 -o $PROJECTID-$PRIMER-rc/$PROJECTID-$PRIMER-paired.txt
+    time tronko-assign -r -f $PROJECTID-$PRIMER/tronkodb/reference_tree.txt.gz -a $PROJECTID-$PRIMER/tronkodb/$PRIMER.fasta -p -z -w -1 $PROJECTID-$PRIMER-rc/$PROJECTID-$PRIMER-paired_F.fasta -2 $PROJECTID-$PRIMER-rc/$PROJECTID-$PRIMER-paired_R.fasta -6 -C 1 -c $LCA -o $PROJECTID-$PRIMER-rc/$PROJECTID-$PRIMER-paired.txt
 
     # filter tronko output
     /mnt/chisquared_filter.pl $PROJECTID-$PRIMER-rc/$PROJECTID-$PRIMER-paired.txt $PROJECTID-$PRIMER-rc/$PROJECTID-$PRIMER-paired_F.fasta $PROJECTID-$PRIMER-rc/$PROJECTID-$PRIMER-paired_R.fasta $PROJECTID-$PRIMER-rc/$PROJECTID-$PRIMER-paired_F.asv $PROJECTID-$PRIMER-rc/$PROJECTID-$PRIMER-paired_R.asv
@@ -343,15 +344,15 @@ then
     fi
 
     # run tronko assign
-    time tronko-assign -r -f $PROJECTID-$PRIMER/tronkodb/reference_tree.txt.gz -a $PROJECTID-$PRIMER/tronkodb/$PRIMER.fasta -s -w -g $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-unpaired_F.fasta -6 -C 1 -c 5 -o $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-unpaired_F.txt
+    time tronko-assign -r -f $PROJECTID-$PRIMER/tronkodb/reference_tree.txt.gz -a $PROJECTID-$PRIMER/tronkodb/$PRIMER.fasta -s -w -g $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-unpaired_F.fasta -6 -C 1 -c $LCA -o $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-unpaired_F.txt
 
     # Count rows with values less than 5 in the 4th column in v1 of unpaired_F
     count_1=$(awk -F '\t' '$4 < 5 { count++ } END { print count }' "$PROJECTID-$PRIMER/$PROJECTID-$PRIMER-unpaired_F.txt")
     if [[ -z "$count_1" ]]; then
         count_1=0
     fi
     # run tronko assign unpaired_F v2 (rc)
-    time tronko-assign -r -f $PROJECTID-$PRIMER/tronkodb/reference_tree.txt.gz -a $PROJECTID-$PRIMER/tronkodb/$PRIMER.fasta -s -w -g $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-unpaired_F.fasta -6 -C 1 -c 5 -v -o $PROJECTID-$PRIMER-rc/$PROJECTID-$PRIMER-unpaired_F.txt
+    time tronko-assign -r -f $PROJECTID-$PRIMER/tronkodb/reference_tree.txt.gz -a $PROJECTID-$PRIMER/tronkodb/$PRIMER.fasta -s -w -g $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-unpaired_F.fasta -6 -C 1 -c $LCA -v -o $PROJECTID-$PRIMER-rc/$PROJECTID-$PRIMER-unpaired_F.txt
 
     # Count rows with values less than 5 in the 4th column in v2 (rc) of unpaired_F
     count_2=$(awk -F '\t' '$4 < 5 { count++ } END { print count }' "$PROJECTID-$PRIMER-rc/$PROJECTID-$PRIMER-unpaired_F.txt")
@@ -439,15 +440,15 @@ then
     fi
 
     # run tronko assign
-    time tronko-assign -r -f $PROJECTID-$PRIMER/tronkodb/reference_tree.txt.gz -a $PROJECTID-$PRIMER/tronkodb/$PRIMER.fasta -s -w -g $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-unpaired_R.fasta -6 -C 1 -c 5 -v -o $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-unpaired_R.txt
+    time tronko-assign -r -f $PROJECTID-$PRIMER/tronkodb/reference_tree.txt.gz -a $PROJECTID-$PRIMER/tronkodb/$PRIMER.fasta -s -w -g $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-unpaired_R.fasta -6 -C 1 -c $LCA -v -o $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-unpaired_R.txt
 
     # Count rows with values less than 5 in the 5th column in v1 of unpaired_R
     count_1=$(awk -F '\t' '$5 < 5 { count++ } END { print count }' "$PROJECTID-$PRIMER/$PROJECTID-$PRIMER-unpaired_R.txt")
     if [[ -z "$count_1" ]]; then
         count_1=0
     fi
     # run tronko assign unpaired_R v2 (rc)
-    time tronko-assign -r -f $PROJECTID-$PRIMER/tronkodb/reference_tree.txt.gz -a $PROJECTID-$PRIMER/tronkodb/$PRIMER.fasta -s -w -g $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-unpaired_R.fasta -6 -C 1 -c 5 -o $PROJECTID-$PRIMER-rc/$PROJECTID-$PRIMER-unpaired_R.txt
+    time tronko-assign -r -f $PROJECTID-$PRIMER/tronkodb/reference_tree.txt.gz -a $PROJECTID-$PRIMER/tronkodb/$PRIMER.fasta -s -w -g $PROJECTID-$PRIMER/$PROJECTID-$PRIMER-unpaired_R.fasta -6 -C 1 -c $LCA -o $PROJECTID-$PRIMER-rc/$PROJECTID-$PRIMER-unpaired_R.txt
 
     # Count rows with values less than 5 in the 5th column in v2 (rc) of unpaired_R
     count_2=$(awk -F '\t' '$5 < 5 { count++ } END { print count }' "$PROJECTID-$PRIMER-rc/$PROJECTID-$PRIMER-unpaired_R.txt")