--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/w4mjoinpn.sh	Sun Oct 29 10:05:05 2017 -0400
@@ -0,0 +1,140 @@
+#!/bin/bash
+# join positive and negative ionization-mode XCMS datasets for a common set of samples
+# summary:
+#   - parse and validate arguments (or abort)
+#   - check that the same samples are present in the same order in both the positive and negative mode data matrices (or abort)
+
+# Parse arguments
+#   ref: https://stackoverflow.com/questions/192249/how-do-i-parse-command-line-arguments-in-bash/14203146#14203146
+POSITIONAL=()
+while [[ $# -gt 0 ]]; do
+  key="$1"
+  case $key in
+    dmpos)
+      DMPOS="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    dmneg)
+      DMNEG="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    dmout)
+      DMOUT="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    smpos)
+      SMPOS="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    smneg)
+      SMNEG="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    smout)
+      SMOUT="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    vmpos)
+      VMPOS="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    vmneg)
+      VMNEG="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    vmout)
+      VMOUT="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    *)    # unknown option
+      POSITIONAL+=("$1") # save it in an array for later
+      shift # past argument
+      ;;
+  esac
+done
+set -- "${POSITIONAL[@]}" # restore positional parameters
+if [[ -n $1 ]]; then
+  echo "unexpected argument $1"
+  echo "arguments supplied: $@"
+  exit 1
+fi
+
+# Validate that we got the expected args
+set -- ${DMPOS} ${DMNEG} ${DMOUT} ${SMPOS} ${SMNEG} ${SMOUT} ${VMPOS} ${VMNEG} ${VMOUT}
+if [[ ! -n $9 ]]; then
+  echo "expecting nine arguments"
+  echo "parsed arguments: $@"
+  exit 1
+fi
+
+# Show them what we got
+echo "dataMatrix       positive_mode ${DMPOS}"
+echo "dataMatrix       negative_mode ${DMNEG}"
+echo "dataMatrix       joined_modes  ${DMOUT}"
+echo "sampleMetadata   positive_mode ${SMPOS}"
+echo "sampleMetadata   negative_mode ${SMNEG}"
+echo "sampleMetadata   joined_modes  ${SMOUT}"
+echo "variableMetadata positive_mode ${VMPOS}"
+echo "variableMetadata negative_mode ${VMNEG}"
+echo "variableMetadata joined_modes  ${VMOUT}"
+
+# Check that sample names are the same, in the same order, for the dataMatrix in both datasets
+if [ "$( head -n 1 ${DMPOS} )" != "$( head -n 1 ${DMNEG} )" ]; then echo sample names in dataMatrix files differ;     exit 1; fi
+# Check that sample names are the same, in the same order, for the sampleMetadata in both datasets
+if [ "$( cut  -f 1 ${SMPOS} )" != "$( cut  -f 1 ${SMNEG} )" ]; then echo sample names in sampleMetadata files differ; exit 1; fi
+
+# Concatenate variableMetadata datasets to respective output file
+cat  <( head -n 1 ${VMNEG} )   <( sed -n -e '1 d; s/^/N/; p;' ${VMNEG} )  <( sed -n -e '1 d; s/^/P/; p;' ${VMPOS} ) > ${VMOUT}
+
+# Concatenate dataMatrix datasets to respective output file
+cat  <( head -n 1 ${DMNEG} )   <( sed -n -e '1 d; s/^/N/; p;' ${DMNEG} )  <( sed -n -e '1 d; s/^/P/; p;' ${DMPOS} ) > ${DMOUT}
+
+# Determine whether negative ionization-mode sampleMetadata file's column three is titled "polarity"
+
+# find the ordinal number of the first column named "polarity" of the negative ionization-mode sampleMetadata file, if any
+set -- `head -n 1 ${SMNEG}`
+POLARITY=0
+MAXCOUNT=0
+while [[ $# -gt 0 ]]; do
+  MAXCOUNT=$(( MAXCOUNT + 1 ))
+  key="$1"
+  case $key in
+    polarity)
+      if [ $POLARITY -eq 0 ]; then POLARITY=${MAXCOUNT}; fi
+      shift # past argument
+      ;;
+    *)    # unknown option
+      shift # past argument
+      ;;
+  esac
+done
+echo "Polarity is in column $POLARITY of ${SMNEG}"
+echo "There  are  $MAXCOUNT columns  in  ${SMNEG}"
+
+# Copy sampleMetadata from negative ionization-mode to output file, replacing polarity if possible
+if [ ${POLARITY} -gt 1 ]; then
+  COLBEFORE=$(( POLARITY - 1 ))
+  COLAFTER=$(( POLARITY + 1 ))
+  # Replace all entries in column three of negative ionization-mode sampleMetadata file with "posneg" in respective output file
+  if [ ${POLARITY} -lt ${MAXCOUNT} ]; then
+    # Handle the case where polarity is not in the last column
+    paste <( cut -f 1-${COLBEFORE} ${SMNEG} ) <( cut -f ${POLARITY} ${SMNEG} | sed -n -e '2,$ s/.*/posneg/; p;' )  <( cut -f ${COLAFTER}- ${SMNEG} )  > ${SMOUT}
+  else
+    # Handle the case where polarity is in the last column
+    paste <( cut -f 1-${COLBEFORE} ${SMNEG} ) <( cut -f ${POLARITY} ${SMNEG} | sed -n -e '2,$ s/.*/posneg/; p;' )  > ${SMOUT}
+  fi
+else
+  # Handle the case where polarity was not found: Copy negative ionization-mode sampleMetadata file to the respective output file
+  cp ${SMNEG} ${SMOUT}
+fi
+
+exit 0