jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified June 22, 2016
jpayne@69: 
jpayne@69: Description:  Summarizes the stats output of Seal for evaluation of 
jpayne@69: cross-contamination.  The intended use is to map multiple libraries or 
jpayne@69: assemblies, of different multiplexed organisms, to a concatenated reference 
jpayne@69: containing one fused scaffold per organism.  This will convert all of the 
jpayne@69: resulting stats files (one per library) to a single text file, with multiple 
jpayne@69: columns, indicating how much of the input hit the primary versus nonprimary 
jpayne@69: scaffolds.
jpayne@69: 
jpayne@69: If ingoresametaxa or ignoresamebarcode are used, ref names must be 
jpayne@69: in this format:
jpayne@69: barcode,library,tax,location
jpayne@69: For example:
jpayne@69: 6-G,N0296,gammaproteobacteria_bacterium,deep_ocean
jpayne@69: 
jpayne@69: Usage:  summarizeseal.sh in=<file,file...> out=<file>
jpayne@69: 
jpayne@69: You can alternately run 'summarizeseal.sh *.txt out=out.txt'
jpayne@69: 
jpayne@69: Parameters:
jpayne@69: in=<file>              A list of stats files, or a text file containing one stats file name per line.
jpayne@69: out=<file>             Destination for summary.
jpayne@69: printtotal=t           (pt) Print a line summarizing the total contamination rate of all assemblies.
jpayne@69: ignoresametaxa=f       Ignore secondary hits sharing taxonomy. 
jpayne@69: ignoresamebarcode=f    Ignore secondary hits sharing a barcode.
jpayne@69: ignoresamelocation=f   Ignore secondary hits sharing a sampling site.
jpayne@69: totaldenominator=f     (td) Use all bases as denominator rather than mapped bases.
jpayne@69: 
jpayne@69: Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
jpayne@69: "
jpayne@69: }
jpayne@69: 
jpayne@69: #This block allows symlinked shellscripts to correctly set classpath.
jpayne@69: pushd . > /dev/null
jpayne@69: DIR="${BASH_SOURCE[0]}"
jpayne@69: while [ -h "$DIR" ]; do
jpayne@69:   cd "$(dirname "$DIR")"
jpayne@69:   DIR="$(readlink "$(basename "$DIR")")"
jpayne@69: done
jpayne@69: cd "$(dirname "$DIR")"
jpayne@69: DIR="$(pwd)/"
jpayne@69: popd > /dev/null
jpayne@69: 
jpayne@69: #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
jpayne@69: CP="$DIR""current/"
jpayne@69: 
jpayne@69: z="-Xmx120m"
jpayne@69: set=0
jpayne@69: 
jpayne@69: if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
jpayne@69: 	usage
jpayne@69: 	exit
jpayne@69: fi
jpayne@69: 
jpayne@69: calcXmx () {
jpayne@69: 	source "$DIR""/calcmem.sh"
jpayne@69: 	setEnvironment
jpayne@69: 	parseXmx "$@"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: summarizeseal() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP driver.SummarizeSealStats $@"
jpayne@69: #	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: summarizeseal "$@"