Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/bbest.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@69 | 1 #!/bin/bash |
| jpayne@69 | 2 |
| jpayne@69 | 3 usage(){ |
| jpayne@69 | 4 echo " |
| jpayne@69 | 5 Written by Brian Bushnell |
| jpayne@69 | 6 Last modified November 4, 2015 |
| jpayne@69 | 7 |
| jpayne@69 | 8 Description: Calculates EST (expressed sequence tags) capture by an assembly from a sam file. |
| jpayne@69 | 9 Designed to use BBMap output generated with these flags: k=13 maxindel=100000 customtag ordered |
| jpayne@69 | 10 |
| jpayne@69 | 11 Usage: bbest.sh in=<sam file> out=<stats file> |
| jpayne@69 | 12 |
| jpayne@69 | 13 Parameters: |
| jpayne@69 | 14 in=<file> Specify a sam file (or stdin) containing mapped ests. |
| jpayne@69 | 15 out=<file> Specify the output stats file (default is stdout). |
| jpayne@69 | 16 ref=<file> Specify the reference file (optional). |
| jpayne@69 | 17 est=<file> Specify the est fasta file (optional). |
| jpayne@69 | 18 fraction=0.98 Min fraction of bases mapped to ref to be |
| jpayne@69 | 19 considered 'all mapped'. |
| jpayne@69 | 20 |
| jpayne@69 | 21 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. |
| jpayne@69 | 22 " |
| jpayne@69 | 23 } |
| jpayne@69 | 24 |
| jpayne@69 | 25 #This block allows symlinked shellscripts to correctly set classpath. |
| jpayne@69 | 26 pushd . > /dev/null |
| jpayne@69 | 27 DIR="${BASH_SOURCE[0]}" |
| jpayne@69 | 28 while [ -h "$DIR" ]; do |
| jpayne@69 | 29 cd "$(dirname "$DIR")" |
| jpayne@69 | 30 DIR="$(readlink "$(basename "$DIR")")" |
| jpayne@69 | 31 done |
| jpayne@69 | 32 cd "$(dirname "$DIR")" |
| jpayne@69 | 33 DIR="$(pwd)/" |
| jpayne@69 | 34 popd > /dev/null |
| jpayne@69 | 35 |
| jpayne@69 | 36 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" |
| jpayne@69 | 37 CP="$DIR""current/" |
| jpayne@69 | 38 |
| jpayne@69 | 39 z="-Xmx120m" |
| jpayne@69 | 40 z2="-Xms120m" |
| jpayne@69 | 41 set=0 |
| jpayne@69 | 42 |
| jpayne@69 | 43 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 44 usage |
| jpayne@69 | 45 exit |
| jpayne@69 | 46 fi |
| jpayne@69 | 47 |
| jpayne@69 | 48 calcXmx () { |
| jpayne@69 | 49 source "$DIR""/calcmem.sh" |
| jpayne@69 | 50 setEnvironment |
| jpayne@69 | 51 parseXmx "$@" |
| jpayne@69 | 52 } |
| jpayne@69 | 53 calcXmx "$@" |
| jpayne@69 | 54 |
| jpayne@69 | 55 function bbest() { |
| jpayne@69 | 56 local CMD="java $EA $EOOM $z -cp $CP jgi.SamToEst $@" |
| jpayne@69 | 57 # echo $CMD >&2 |
| jpayne@69 | 58 eval $CMD |
| jpayne@69 | 59 } |
| jpayne@69 | 60 |
| jpayne@69 | 61 bbest "$@" |