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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 Jan 29, 2020
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7
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8 Description: Adds, removes, or replaces SSU sequence of existing sketches.
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9 Sketches and SSU fasta files must be annotated with TaxIDs.
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10
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11 Usage: addssu.sh in=a.sketch out=b.sketch 16S=16S.fa 18S=18S.fa
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12
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13 Standard parameters:
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14 in=<file> Input sketch file.
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15 out=<file> Output sketch file.
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16
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17 Additional files (optional):
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18 16S=<file> A fasta file of 16S sequences. These should be renamed
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19 so that they start with tid|# where # is the taxID.
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20 Should not contain organelle rRNA.
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21 18S=<file> A fasta file of 18S sequences. These should be renamed
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22 so that they start with tid|# where # is the taxID.
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23 Should not contain organelle rRNA.
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24 tree=auto Path to TaxTree, if performing prok/euk-specific operations.
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25
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26 Processing parameters:
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27 preferSSUMap=f
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28 preferSSUMapEuks=f
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29 preferSSUMapProks=f
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30 SSUMapOnly=f
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31 SSUMapOnlyEuks=f
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32 SSUMapOnlyProks=f
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33 clear16S=f
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34 clear18S=f
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35 clear16SEuks=f
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36 clear18SEuks=f
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37 clear16SProks=f
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38 clear18SProks=f
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39
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40
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41 Java Parameters:
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42 -Xmx This will set Java's memory usage, overriding autodetection.
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43 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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44 The max is typically 85% of physical memory.
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45 -da Disable assertions.
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46
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47 For more detailed information, please read /bbmap/docs/guides/BBSketchGuide.txt.
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48 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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49 "
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50 }
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51
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52 #This block allows symlinked shellscripts to correctly set classpath.
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53 pushd . > /dev/null
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54 DIR="${BASH_SOURCE[0]}"
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55 while [ -h "$DIR" ]; do
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56 cd "$(dirname "$DIR")"
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57 DIR="$(readlink "$(basename "$DIR")")"
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58 done
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59 cd "$(dirname "$DIR")"
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60 DIR="$(pwd)/"
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61 popd > /dev/null
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62
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63 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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64 CP="$DIR""current/"
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65
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66 z="-Xmx4g"
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67 z2="-Xms4g"
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68 set=0
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69
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70 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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71 usage
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72 exit
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73 fi
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74
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75 calcXmx () {
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76 source "$DIR""/calcmem.sh"
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77 setEnvironment
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78 parseXmx "$@"
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79 if [[ $set == 1 ]]; then
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80 return
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81 fi
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82 #freeRam 3200m 84
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83 #z="-Xmx${RAM}m"
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84 #z2="-Xms${RAM}m"
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85 }
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86 calcXmx "$@"
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87
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88 sendsketch() {
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89 local CMD="java $EA $EOOM $z -cp $CP sketch.AddSSU $@"
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90 echo $CMD >&2
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91 eval $CMD
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92 }
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93
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94 sendsketch "$@"
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