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jpayne@69
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1 #!/bin/bash
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2
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3 usage(){
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4 echo "
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5 Written by Brian Bushnell
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6 Last modified December 19, 2019
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7
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8 Description: Analyzes sketch results from query, ref, ani format.
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9
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10 Usage: analyzesketchresults.sh in=<file> out=<outfile>
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11
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12
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13 Parameters and their defaults:
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14
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15 in=<file> Required input file of Sketch results in 3column format.
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16 in2=<file> Optional second input file of Sketch results in amino mode.
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17 out=stdout.txt Output file for summary of per-tax-level averages.
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18 outaccuracy=<file> Output file for accuracy results; requires query taxIDs and printcal.
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19 outmap=<file> Output file for ANI vs AAI. Requires in2.
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20 bbsketch Parse BBSketch output format (default).
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21 mash Parse Mash output format. Files should be named like this:
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22 tid_511145_Escherichia_coli_str._K-12_substr._MG1655.fa.gz
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23 blast Parse Blast output format (TODO).
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24
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25 ow=f (overwrite) Overwrites files that already exist.
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26 app=f (append) Append to files that already exist.
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27
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28 Java Parameters:
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29 -Xmx This will set Java's memory usage, overriding autodetection.
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30 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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31 The max is typically 85% of physical memory.
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32 -eoom This flag will cause the process to exit if an out-of-memory exception occurs. Requires Java 8u92+.
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33 -da Disable assertions.
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34
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35 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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36 "
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37 }
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38
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39 #This block allows symlinked shellscripts to correctly set classpath.
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40 pushd . > /dev/null
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41 DIR="${BASH_SOURCE[0]}"
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42 while [ -h "$DIR" ]; do
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43 cd "$(dirname "$DIR")"
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44 DIR="$(readlink "$(basename "$DIR")")"
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45 done
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46 cd "$(dirname "$DIR")"
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47 DIR="$(pwd)/"
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48 popd > /dev/null
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49
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50 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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51 CP="$DIR""current/"
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52
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53 z="-Xmx300m"
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54 z="-Xms300m"
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55 set=0
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56
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57 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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58 usage
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59 exit
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60 fi
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61
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62 calcXmx () {
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63 source "$DIR""/calcmem.sh"
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64 setEnvironment
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65 parseXmx "$@"
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66 }
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67 calcXmx "$@"
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68
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69 function analyzesketchresults() {
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70 local CMD="java $EA $EOOM $z $z2 -cp $CP sketch.AnalyzeSketchResults $@"
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71 echo $CMD >&2
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72 eval $CMD
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73 }
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74
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75 analyzesketchresults "$@"
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