add script to extract memote scores

Author: pwendering

code/bash/extract-scores-memote.sh

@@ -0,0 +1,42 @@
+#!/bin/bash
+# Extract memote scores from html report files.
+# Prints the result to stdout.
+
+get_score() {
+  # Input 1 is filename
+  # Input 2 is query
+  echo $(cat $1 | grep -A2 "$2" | grep -o "[0-9][0-9\.\,]*")
+}
+
+# isolate ID
+ID=$(head -1 $1)
+
+# stoichiometric consistency
+s_con=$(get_score $1 "Stoichiometric Consistency")
+
+# mass balance
+m_bal=$(get_score $1 "Mass Balance")
+
+# charge balance
+c_bal=$(get_score $1 "Charge Balance")
+
+# metabolite connectivity
+m_conn=$(get_score $1 "Metabolite Connectivity")
+
+# unbounded flux
+ubd_flx=$(get_score $1 "Unbounded Flux In Default Medium")
+
+# stoichiometrically balanced cycles
+sbc=$(get_score $1 "Stoichiometrically Balanced Cycles")
+
+# universally blocked reactions
+blocked=$(get_score $1 "Universally Blocked Reactions")
+
+# consistency	subscore
+cons_sub=$(get_score $1 "Sub Total" | grep -m 1 -o "[0-9][0-9\.]*" | head -n 1)
+
+# total score
+tot_score=$(get_score $1 "Total Score" | grep -m 1 -o "[0-9][0-9\.]*" | head -n 1)
+
+
+echo -e "$ID\t$s_con\t$m_bal\t$c_bal\t$m_conn\t$ubd_flx\t$sbc\t$blocked\t$cons_sub\t$tot_score"