diff misc/bug1/cmp.sh @ 18:e4d75f9efb90 draft

planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/misc/bug1/cmp.sh	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,43 @@
+#!/usr/bin/env bash
+if [ x$BASH = x ] || [ ! $BASH_VERSINFO ] || [ $BASH_VERSINFO -lt 4 ]; then
+  echo "Error: Must use bash version 4+." >&2
+  exit 1
+fi
+set -ue
+
+TmpSscsBefore="tmp.sscs.before.fa"
+TmpSscsAfter="tmp.sscs.after.fa"
+TmpMsa="tmp.family.msa.tsv"
+
+Usage="Usage: \$ $(basename $0) diff.family.msa.tsv diff.sscs.before.fa diff.sscs.after.fa > cmp.txt"
+
+function main {
+  if [[ $# -lt 3 ]] || [[ $1 == '-h' ]]; then
+    fail "$Usage"
+  else
+    msa_input="$1"
+    sscs_before="$2"
+    sscs_after="$3"
+  fi
+
+  lines=$(cat $sscs_before | wc -l)
+  choice=$(python -c "import random; print 2*random.randint(1, $lines/2)")
+
+  echo $lines $choice >&2
+
+  head -n $choice $sscs_before | tail -n 2 > $TmpSscsBefore
+  head -n $choice $sscs_after | tail -n 2 > $TmpSscsAfter
+  cat $msa_input | ../msa_sscs_matcher.py $TmpSscsBefore > $TmpMsa
+
+  tail -n +2 $TmpSscsBefore
+  tail -n +2 $TmpSscsAfter
+  echo
+  cut -f 5,6 $TmpMsa
+}
+
+function fail {
+  echo "$@" >&2
+  exit 1
+}
+
+main "$@"