Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/countgc.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 January 21, 2015 |
| jpayne@69 | 7 |
| jpayne@69 | 8 Description: Counts GC content of reads or scaffolds. |
| jpayne@69 | 9 |
| jpayne@69 | 10 Usage: countgc in=<input> out=<output> format=<format> |
| jpayne@69 | 11 |
| jpayne@69 | 12 Input may be stdin or a fasta or fastq file, compressed or uncompressed. |
| jpayne@69 | 13 Output (which is optional) is tab-delimited. |
| jpayne@69 | 14 format=1: name length A C G T N |
| jpayne@69 | 15 format=2: name GC |
| jpayne@69 | 16 format=4: name length GC |
| jpayne@69 | 17 Note that in format 1, A+C+G+T=1 even when N is nonzero. |
| jpayne@69 | 18 |
| jpayne@69 | 19 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. |
| jpayne@69 | 20 " |
| jpayne@69 | 21 } |
| jpayne@69 | 22 |
| jpayne@69 | 23 #This block allows symlinked shellscripts to correctly set classpath. |
| jpayne@69 | 24 pushd . > /dev/null |
| jpayne@69 | 25 DIR="${BASH_SOURCE[0]}" |
| jpayne@69 | 26 while [ -h "$DIR" ]; do |
| jpayne@69 | 27 cd "$(dirname "$DIR")" |
| jpayne@69 | 28 DIR="$(readlink "$(basename "$DIR")")" |
| jpayne@69 | 29 done |
| jpayne@69 | 30 cd "$(dirname "$DIR")" |
| jpayne@69 | 31 DIR="$(pwd)/" |
| jpayne@69 | 32 popd > /dev/null |
| jpayne@69 | 33 |
| jpayne@69 | 34 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" |
| jpayne@69 | 35 CP="$DIR""current/" |
| jpayne@69 | 36 |
| jpayne@69 | 37 z="-Xmx120m" |
| jpayne@69 | 38 set=0 |
| jpayne@69 | 39 |
| jpayne@69 | 40 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 41 usage |
| jpayne@69 | 42 exit |
| jpayne@69 | 43 fi |
| jpayne@69 | 44 |
| jpayne@69 | 45 calcXmx () { |
| jpayne@69 | 46 source "$DIR""/calcmem.sh" |
| jpayne@69 | 47 setEnvironment |
| jpayne@69 | 48 parseXmx "$@" |
| jpayne@69 | 49 } |
| jpayne@69 | 50 calcXmx "$@" |
| jpayne@69 | 51 |
| jpayne@69 | 52 countgc() { |
| jpayne@69 | 53 local CMD="java $EA $EOOM $z -cp $CP jgi.CountGC $@" |
| jpayne@69 | 54 echo $CMD >&2 |
| jpayne@69 | 55 eval $CMD |
| jpayne@69 | 56 } |
| jpayne@69 | 57 |
| jpayne@69 | 58 countgc "$@" |