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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 4, 2019
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7
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8 Description: Aligns SSUs to each other and reports identity.
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9 This requires sequences annotated with a taxID in their header.
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10
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11 Usage: comparessu.sh in=<input file> out=<output file>
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12
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13 Input may be fasta or fastq, compressed or uncompressed.
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14
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15 Standard parameters:
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16 in=<file> Input sequences.
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17 out=<file> Output data.
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18 t= Set the number of threads; default is logical processors.
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19 overwrite=f (ow) Set to false to force the program to abort rather than
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20 overwrite an existing file.
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21 showspeed=t (ss) Set to 'f' to suppress display of processing speed.
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22 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
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23 level; lower compression is faster.
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24 reads=-1 If positive, quit after this many sequences.
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25
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26 Processing parameters:
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27 ata=f Do an all-to-all comparison. Otherwise, each sequence will
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28 only be compared to one other randomly-selected sequence
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29 per taxonomic level.
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30 minlen=0 Ignore sequences shorter than this.
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31 maxlen=BIG Ignore sequences longer than this.
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32 maxns=-1 If positive, ignore sequences with more than this many Ns.
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33
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34
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35 Java Parameters:
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36 -Xmx This will set Java's memory usage, overriding autodetection.
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37 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
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38 specify 200 megs. The max is typically 85% of physical memory.
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39 -eoom This flag will cause the process to exit if an out-of-memory
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40 exception occurs. Requires Java 8u92+.
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41 -da Disable assertions.
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42
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43 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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44 "
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45 }
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46
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47 #This block allows symlinked shellscripts to correctly set classpath.
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48 pushd . > /dev/null
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49 DIR="${BASH_SOURCE[0]}"
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50 while [ -h "$DIR" ]; do
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51 cd "$(dirname "$DIR")"
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52 DIR="$(readlink "$(basename "$DIR")")"
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53 done
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54 cd "$(dirname "$DIR")"
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55 DIR="$(pwd)/"
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56 popd > /dev/null
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57
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58 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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59 CP="$DIR""current/"
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60
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61 z="-Xmx4g"
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62 z2="-Xms4g"
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63 set=0
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64
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65 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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66 usage
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67 exit
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68 fi
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69
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70 calcXmx () {
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71 source "$DIR""/calcmem.sh"
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72 setEnvironment
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73 parseXmx "$@"
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74 if [[ $set == 1 ]]; then
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75 return
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76 fi
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77 freeRam 4000m 84
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78 z="-Xmx${RAM}m"
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79 z2="-Xms${RAM}m"
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80 }
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81 calcXmx "$@"
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82
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83 comparessu() {
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84 local CMD="java $EA $EOOM $z -cp $CP sketch.CompareSSU $@"
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85 echo $CMD >&2
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86 eval $CMD
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87 }
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88
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89 comparessu "$@"
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