tsvsummary for bash

tsv/tsvsummary

@@ -0,0 +1,61 @@
+#!/bin/bash
+
+set -e
+function usage {
+echo -e ' tsvsummary, a CSVSummary clone for the command line. 
+Depends on csvkit and ncsv
+
+Usage:   tsvsummary [-c column] [-t type] tsv_file
+   -c    name of the column to use as clusterCol 
+         (produce as many lines as column has unique values)
+   -t    Type of statistics: mean, max, min, sum, stdev, nas, unique
+   -h    Help
+'
+
+}
+TYPEOF=mean
+TYPELIST=( mean max min sum stdev nas unique )
+while getopts c:ht: opt
+do  case "$opt" in
+    c)
+        LABEL=$OPTARG
+    ;;
+    t)
+        TYPEOF=$( echo $OPTARG | tr '[:upper:]' '[:lower:]' )
+    ;;
+    h)
+        usage
+        exit
+    ;;
+    \?)
+      exit
+      ;;
+    esac
+done
+shift $(( ${OPTIND} - 1 ));
+
+for type in "${TYPELIST[@]}"
+do if [ "$type" = "$TYPEOF" ]; then TYPEFOUND=1;fi
+done
+[[ -z "$TYPEFOUND" ]] && ( echo Statistics type $TYPEOF not recognized, valid ones: ${TYPELIST[@]}; exit 1 )
+
+if [ -z "$1" ]
+then usage
+     echo No file name provided
+     exit 1
+fi
+
+if [ -z "$LABEL" ]
+then ncsv --stat "$1" | sed -n "1p;/^$TYPEOF/Ip"
+     exit
+else
+     IFS=$'\n'
+     UNIQUE=( $( csvcut -t -c "$LABEL" "$1" | tail -n +2 | sort -uV ) )
+     HEADER=$( csvcut -t -C "$LABEL" "$1" | head -n 1 | ncsv -i, -d"\t" )
+     echo -e "$LABEL\tStatistic\t$HEADER"
+     
+     for (( i=0; i<${#UNIQUE[@]}; i++ ))
+     do  echo -ne "${UNIQUE[$i]}\t"
+         csvgrep -t -c "$LABEL" -m "${UNIQUE[$i]}" "$1" | csvcut -C "$LABEL" | ncsv -i, --stat | sed -n "/^$TYPEOF/Ip"
+     done
+fi