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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 July 31, 2015
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7
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8 Description: Reduces Silva entries down to one entry per taxa (the first).
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9 This is accomplished by splitting the semicolon-delimited name on semicolons,
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10 and assuming everything is in the form of:
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11 kingdom;phylum;class;order;family;genus;species
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12 ...so it's not very reliable.
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13
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14 Usage: reducesilva.sh in=<file> out=<file> column=<1>
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15
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16 Parameters:
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17 column The taxonomic level. 0=species, 1=genus, etc.
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18 ow=f (overwrite) Overwrites files that already exist.
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19 zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
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20 fastawrap=70 Length of lines in fasta output.
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21
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22 Sampling parameters:
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23 reads=-1 Set to a positive number to only process this many INPUT sequences, then quit.
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24
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25 Java Parameters:
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26 -Xmx This will set Java's memory usage, overriding autodetection.
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27 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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28 The max is typically 85% of physical memory.
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29 -eoom This flag will cause the process to exit if an out-of-memory
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30 exception occurs. Requires Java 8u92+.
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31 -da Disable assertions.
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32
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33 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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34 "
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35 }
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36
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37 #This block allows symlinked shellscripts to correctly set classpath.
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38 pushd . > /dev/null
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39 DIR="${BASH_SOURCE[0]}"
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40 while [ -h "$DIR" ]; do
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41 cd "$(dirname "$DIR")"
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42 DIR="$(readlink "$(basename "$DIR")")"
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43 done
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44 cd "$(dirname "$DIR")"
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45 DIR="$(pwd)/"
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46 popd > /dev/null
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47
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48 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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49 CP="$DIR""current/"
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50
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51 z="-Xmx1g"
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52 set=0
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53
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54 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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55 usage
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56 exit
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57 fi
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58
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59 calcXmx () {
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60 source "$DIR""/calcmem.sh"
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61 setEnvironment
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62 parseXmx "$@"
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63 }
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64 calcXmx "$@"
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65
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66 function reducesilva() {
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67 local CMD="java $EA $EOOM $z -cp $CP driver.ReduceSilva $@"
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68 echo $CMD >&2
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69 eval $CMD
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70 }
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71
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72 reducesilva "$@"
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