Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/tetramerfreq.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
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| children |
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| 67:0e9998148a16 | 69:33d812a61356 |
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| 1 #!/bin/bash | |
| 2 | |
| 3 usage(){ | |
| 4 echo " | |
| 5 Written by Shijie Yao | |
| 6 Last modified May 31, 2018 | |
| 7 | |
| 8 Description: DNA Tetramer analysis. | |
| 9 DNA tetramers are counted for each sub-sequence of window size in the sequence. | |
| 10 The window slides along the sequence by the step length. | |
| 11 Sub-sequence shorter than the window size is ignored. Tetramers containing N are ignored. | |
| 12 | |
| 13 Usage: TetramerFreq.sh in=<input file> out=<output file> step=500 window=2000 | |
| 14 | |
| 15 Input may be fasta or fastq, compressed or uncompressed. | |
| 16 | |
| 17 Standard parameters: | |
| 18 in=<file> DNA sequence input file | |
| 19 out=<file> Output file name | |
| 20 step/s=INT Step size (default 500) | |
| 21 window/w=INT Window size (default 2kb); <=0 turns windowing off (e.g. short reads) | |
| 22 short=T/F Print lines for sequences shorter than window (default F) | |
| 23 k=INT Kmer length (default 4) | |
| 24 | |
| 25 Java Parameters: | |
| 26 -Xmx This will set Java's memory usage, overriding autodetection. | |
| 27 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will | |
| 28 specify 200 megs. The max is typically 85% of physical memory. | |
| 29 -eoom This flag will cause the process to exit if an out-of-memory | |
| 30 exception occurs. Requires Java 8u92+. | |
| 31 -da Disable assertions. | |
| 32 | |
| 33 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 34 " | |
| 35 } | |
| 36 | |
| 37 #This block allows symlinked shellscripts to correctly set classpath. | |
| 38 pushd . > /dev/null | |
| 39 DIR="${BASH_SOURCE[0]}" | |
| 40 while [ -h "$DIR" ]; do | |
| 41 cd "$(dirname "$DIR")" | |
| 42 DIR="$(readlink "$(basename "$DIR")")" | |
| 43 done | |
| 44 cd "$(dirname "$DIR")" | |
| 45 DIR="$(pwd)/" | |
| 46 popd > /dev/null | |
| 47 | |
| 48 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 49 CP="$DIR""current/" | |
| 50 | |
| 51 z="-Xmx4g" | |
| 52 z2="-Xms4g" | |
| 53 set=0 | |
| 54 | |
| 55 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 56 usage | |
| 57 exit | |
| 58 fi | |
| 59 | |
| 60 calcXmx () { | |
| 61 source "$DIR""/calcmem.sh" | |
| 62 setEnvironment | |
| 63 parseXmx "$@" | |
| 64 if [[ $set == 1 ]]; then | |
| 65 return | |
| 66 fi | |
| 67 freeRam 4000m 84 | |
| 68 z="-Xmx${RAM}m" | |
| 69 z2="-Xms${RAM}m" | |
| 70 } | |
| 71 calcXmx "$@" | |
| 72 | |
| 73 tetramerfreq () { | |
| 74 local CMD="java $EA $EOOM $z -cp $CP jgi.TetramerFrequencies $@" | |
| 75 echo $CMD >&2 | |
| 76 eval $CMD | |
| 77 } | |
| 78 | |
| 79 tetramerfreq "$@" |