Added host-searching shell script

code/03-host.sh

@@ -0,0 +1,45 @@
+# Find Tracheophyta reads putatively belonging to Pseudotsuga menziesii ####
+# Check the validity of the parallelization argument ####
+if [[ $# -lt 1 ]]; then
+  echo 'Error: Please specify the number of threads to launch'
+  exit 1
+fi
+
+if [[ $# -gt 1 ]]; then
+  echo 'Error: Too many arguments have been provided'
+  exit 1
+fi
+
+if [[ $1 =~ [^0-9]+ ]]; then
+  echo 'Error: Only integer arguments are accepted'
+  exit 1
+fi
+
+if [[ $1 -lt 1 ]]; then
+  echo 'Error: At least one thread is needed'
+  exit 1
+fi
+
+# Set or make directories for input, output and log files ####
+in1='03-denoise/filter'
+in2='01-demultiplex'
+out='03-host'
+logs="${out}/logs"
+rm -r $out
+mkdir -p $logs
+touch $out/README.md
+
+# Use ITSxpress to single out Tracheophyta ITS2 (not sure of specificity) ####
+for fwd in $(find $in1 -name "*fun_rev-rc-R1.fq.gz" | grep -f data/nano-k.txt); do
+
+    # Make the name of the corresponding reverse read ####
+    rev=$(echo $fwd | sed 's/R1.fq.gz/R2.fq.gz/')
+
+    # Make a sample name for each file ####
+    sample=$(basename $fwd | awk -F '-' '{print $1"-"$2"-"$3"-"$4"-"$5"-"$6}')
+
+    # Extract ITS ####
+    itsxpress --fastq $fwd --fastq2 $rev --region ITS2 \
+    --taxa Tracheophyta --log $logs/${sample}-itsxpress.txt --outfile ${sample}.fq.gz --threads $1
+
+done