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annotate misc/bug1/cmp.sh @ 4:af383638de66 draft

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planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
author nick
date Mon, 23 Nov 2015 18:44:23 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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4
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1 #!/usr/bin/env bash
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2 if [ x$BASH = x ] || [ ! $BASH_VERSINFO ] || [ $BASH_VERSINFO -lt 4 ]; then
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3 echo "Error: Must use bash version 4+." >&2
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4 exit 1
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5 fi
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6 set -ue
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7
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8 TmpSscsBefore="tmp.sscs.before.fa"
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9 TmpSscsAfter="tmp.sscs.after.fa"
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10 TmpMsa="tmp.family.msa.tsv"
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11
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12 Usage="Usage: \$ $(basename $0) diff.family.msa.tsv diff.sscs.before.fa diff.sscs.after.fa > cmp.txt"
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13
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14 function main {
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15 if [[ $# -lt 3 ]] || [[ $1 == '-h' ]]; then
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16 fail "$Usage"
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17 else
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18 msa_input="$1"
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19 sscs_before="$2"
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20 sscs_after="$3"
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21 fi
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22
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23 lines=$(cat $sscs_before | wc -l)
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24 choice=$(python -c "import random; print 2*random.randint(1, $lines/2)")
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25
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26 echo $lines $choice >&2
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27
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28 head -n $choice $sscs_before | tail -n 2 > $TmpSscsBefore
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29 head -n $choice $sscs_after | tail -n 2 > $TmpSscsAfter
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30 cat $msa_input | ../msa_sscs_matcher.py $TmpSscsBefore > $TmpMsa
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31
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32 tail -n +2 $TmpSscsBefore
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33 tail -n +2 $TmpSscsAfter
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34 echo
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35 cut -f 5,6 $TmpMsa
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36 }
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37
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38 function fail {
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39 echo "$@" >&2
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40 exit 1
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41 }
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42
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43 main "$@"