Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/keepbestcopy.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 Brian Bushnell | |
| 6 Last modified October 4, 2019 | |
| 7 | |
| 8 Description: Discards all but the best copy of a ribosomal gene per TaxID. | |
| 9 Gene sequences should be named like this: >tid|123|whatever | |
| 10 Sequences are selected based on the number of fully defined bases. | |
| 11 | |
| 12 Usage: keepbest.sh in=<input file> out=<output file> rate=<float> | |
| 13 | |
| 14 Input may be fasta or fastq, compressed or uncompressed. | |
| 15 | |
| 16 Standard parameters: | |
| 17 in=<file> Input sequences. | |
| 18 out=<file> Output sequences. | |
| 19 overwrite=f (ow) Set to false to force the program to abort rather than | |
| 20 overwrite an existing file. | |
| 21 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression | |
| 22 level; lower compression is faster. | |
| 23 | |
| 24 Processing parameters: | |
| 25 maxlen=1600 Prefer sequences shorter than this. | |
| 26 | |
| 27 Java Parameters: | |
| 28 -Xmx This will set Java's memory usage, overriding autodetection. | |
| 29 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will | |
| 30 specify 200 megs. The max is typically 85% of physical memory. | |
| 31 -eoom This flag will cause the process to exit if an out-of-memory | |
| 32 exception occurs. Requires Java 8u92+. | |
| 33 -da Disable assertions. | |
| 34 | |
| 35 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 36 " | |
| 37 } | |
| 38 | |
| 39 #This block allows symlinked shellscripts to correctly set classpath. | |
| 40 pushd . > /dev/null | |
| 41 DIR="${BASH_SOURCE[0]}" | |
| 42 while [ -h "$DIR" ]; do | |
| 43 cd "$(dirname "$DIR")" | |
| 44 DIR="$(readlink "$(basename "$DIR")")" | |
| 45 done | |
| 46 cd "$(dirname "$DIR")" | |
| 47 DIR="$(pwd)/" | |
| 48 popd > /dev/null | |
| 49 | |
| 50 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 51 CP="$DIR""current/" | |
| 52 | |
| 53 z="-Xmx8g" | |
| 54 z2="-Xms8g" | |
| 55 set=0 | |
| 56 | |
| 57 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 58 usage | |
| 59 exit | |
| 60 fi | |
| 61 | |
| 62 calcXmx () { | |
| 63 source "$DIR""/calcmem.sh" | |
| 64 setEnvironment | |
| 65 parseXmx "$@" | |
| 66 if [[ $set == 1 ]]; then | |
| 67 return | |
| 68 fi | |
| 69 freeRam 8g 84 | |
| 70 z="-Xmx${RAM}m" | |
| 71 z2="-Xms${RAM}m" | |
| 72 } | |
| 73 calcXmx "$@" | |
| 74 | |
| 75 keepbest() { | |
| 76 local CMD="java $EA $EOOM $z -cp $CP jgi.KeepBestCopy $@" | |
| 77 echo $CMD >&2 | |
| 78 eval $CMD | |
| 79 } | |
| 80 | |
| 81 keepbest "$@" |