Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/summarizescafstats.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
| rev | line source |
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| 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 May 26, 2015 |
| jpayne@69 | 7 |
| jpayne@69 | 8 Description: Summarizes the scafstats output of BBMap for evaluation |
| jpayne@69 | 9 of cross-contamination. The intended use is to map multiple libraries or |
| jpayne@69 | 10 assemblies, of different multiplexed organisms, to a concatenated reference |
| jpayne@69 | 11 containing one fused scaffold per organism. This will convert all of the |
| jpayne@69 | 12 resulting stats files (one per library) to a single text file, with multiple |
| jpayne@69 | 13 columns, indicating how much of the input hit the primary versus nonprimary |
| jpayne@69 | 14 scaffolds. |
| jpayne@69 | 15 |
| jpayne@69 | 16 Usage: summarizescafstats.sh in=<file,file...> out=<file> |
| jpayne@69 | 17 |
| jpayne@69 | 18 You can alternatively use a wildcard, like this: |
| jpayne@69 | 19 summarizescafstats.sh scafstats_*.txt out=summary.txt |
| jpayne@69 | 20 |
| jpayne@69 | 21 Parameters: |
| jpayne@69 | 22 in=<file> A list of stats files, or a text file containing one stats file name per line. |
| jpayne@69 | 23 out=<file> Destination for summary. |
| jpayne@69 | 24 |
| jpayne@69 | 25 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. |
| jpayne@69 | 26 " |
| jpayne@69 | 27 } |
| jpayne@69 | 28 |
| jpayne@69 | 29 #This block allows symlinked shellscripts to correctly set classpath. |
| jpayne@69 | 30 pushd . > /dev/null |
| jpayne@69 | 31 DIR="${BASH_SOURCE[0]}" |
| jpayne@69 | 32 while [ -h "$DIR" ]; do |
| jpayne@69 | 33 cd "$(dirname "$DIR")" |
| jpayne@69 | 34 DIR="$(readlink "$(basename "$DIR")")" |
| jpayne@69 | 35 done |
| jpayne@69 | 36 cd "$(dirname "$DIR")" |
| jpayne@69 | 37 DIR="$(pwd)/" |
| jpayne@69 | 38 popd > /dev/null |
| jpayne@69 | 39 |
| jpayne@69 | 40 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" |
| jpayne@69 | 41 CP="$DIR""current/" |
| jpayne@69 | 42 |
| jpayne@69 | 43 z="-Xmx120m" |
| jpayne@69 | 44 set=0 |
| jpayne@69 | 45 |
| jpayne@69 | 46 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 47 usage |
| jpayne@69 | 48 exit |
| jpayne@69 | 49 fi |
| jpayne@69 | 50 |
| jpayne@69 | 51 calcXmx () { |
| jpayne@69 | 52 source "$DIR""/calcmem.sh" |
| jpayne@69 | 53 setEnvironment |
| jpayne@69 | 54 parseXmx "$@" |
| jpayne@69 | 55 } |
| jpayne@69 | 56 calcXmx "$@" |
| jpayne@69 | 57 |
| jpayne@69 | 58 summarizescafstats() { |
| jpayne@69 | 59 local CMD="java $EA $EOOM $z -cp $CP driver.SummarizeCoverage $@" |
| jpayne@69 | 60 # echo $CMD >&2 |
| jpayne@69 | 61 eval $CMD |
| jpayne@69 | 62 } |
| jpayne@69 | 63 |
| jpayne@69 | 64 summarizescafstats "$@" |