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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 Shijie Yao
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6 Last modified May 31, 2018
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7
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8 Description: DNA Tetramer analysis.
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9 DNA tetramers are counted for each sub-sequence of window size in the sequence.
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10 The window slides along the sequence by the step length.
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11 Sub-sequence shorter than the window size is ignored. Tetramers containing N are ignored.
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12
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13 Usage: TetramerFreq.sh in=<input file> out=<output file> step=500 window=2000
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14
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15 Input may be fasta or fastq, compressed or uncompressed.
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16
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17 Standard parameters:
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18 in=<file> DNA sequence input file
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19 out=<file> Output file name
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20 step/s=INT Step size (default 500)
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21 window/w=INT Window size (default 2kb); <=0 turns windowing off (e.g. short reads)
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22 short=T/F Print lines for sequences shorter than window (default F)
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23 k=INT Kmer length (default 4)
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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
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28 specify 200 megs. 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="-Xmx4g"
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52 z2="-Xms4g"
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53 set=0
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54
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55 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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56 usage
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57 exit
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58 fi
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59
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60 calcXmx () {
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61 source "$DIR""/calcmem.sh"
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62 setEnvironment
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63 parseXmx "$@"
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64 if [[ $set == 1 ]]; then
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65 return
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66 fi
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67 freeRam 4000m 84
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68 z="-Xmx${RAM}m"
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69 z2="-Xms${RAM}m"
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70 }
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71 calcXmx "$@"
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72
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73 tetramerfreq () {
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74 local CMD="java $EA $EOOM $z -cp $CP jgi.TetramerFrequencies $@"
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75 echo $CMD >&2
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76 eval $CMD
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77 }
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78
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79 tetramerfreq "$@"
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