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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 January 22, 2020
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7
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8 Description: Splits a file of various rRNAs into one file per type
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9 (16S, 18S, 5S, 23s).
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10
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11 Usage: splitribo.sh in=<file,file> out=<pattern>
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12
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13 Standard parameters:
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14 in=<file> Input file.
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15 out=<pattern> Output file pattern, such as out_#.fa. The # symbol is
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16 required and will be substituted by the type name, such as
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17 16S, to make out_16S.fa, for example.
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18 overwrite=f (ow) Set to false to force the program to abort rather than
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19 overwrite an existing file.
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20 ziplevel=9 (zl) Set to 1 (lowest) through 9 (max) to change compression
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21 level; lower compression is faster.
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22
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23 types=16S,18S,5S,23S,m16S,m18S,p16S
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24 Align to these sequences. Fewer types is faster. m16S
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25 and m18S are mitochondrial; p16S is plastid (chloroplast).
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26
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27 Processing parameters:
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28 minid=0.59 Ignore alignments with identity lower than this to a
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29 consensus sequences.
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30 refineid=0.70 Refine score by aligning to clade-specific consensus if
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31 the best alignment to a universal consensus is below this.
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32
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33 Java Parameters:
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34 -Xmx This will set Java's memory usage, overriding autodetection.
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35 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
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36 specify 200 megs. The max is typically 85% of physical memory.
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37 -eoom This flag will cause the process to exit if an out-of-memory
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38 exception occurs. Requires Java 8u92+.
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39 -da Disable assertions.
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40
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41 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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42 "
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43 }
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44
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45 #This block allows symlinked shellscripts to correctly set classpath.
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46 pushd . > /dev/null
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47 DIR="${BASH_SOURCE[0]}"
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48 while [ -h "$DIR" ]; do
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49 cd "$(dirname "$DIR")"
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50 DIR="$(readlink "$(basename "$DIR")")"
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51 done
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52 cd "$(dirname "$DIR")"
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53 DIR="$(pwd)/"
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54 popd > /dev/null
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55
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56 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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57 CP="$DIR""current/"
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58
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59 z="-Xmx4g"
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60 z2="-Xms4g"
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61 set=0
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62
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63 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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64 usage
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65 exit
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66 fi
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67
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68 calcXmx () {
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69 source "$DIR""/calcmem.sh"
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70 setEnvironment
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71 parseXmx "$@"
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72 if [[ $set == 1 ]]; then
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73 return
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74 fi
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75 freeRam 4000m 42
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76 z="-Xmx${RAM}m"
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77 z2="-Xms${RAM}m"
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78 }
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79 calcXmx "$@"
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80
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81 mergeribo() {
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82 local CMD="java $EA $EOOM $z -cp $CP prok.SplitRibo $@"
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83 echo $CMD >&2
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84 eval $CMD
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85 }
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86
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87 mergeribo "$@"
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