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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/summarizeseal.sh @ 69:33d812a61356

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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67:0e9998148a16 69:33d812a61356
1 #!/bin/bash
2
3 usage(){
4 echo "
5 Written by Brian Bushnell
6 Last modified June 22, 2016
7
8 Description: Summarizes the stats output of Seal for evaluation of
9 cross-contamination. The intended use is to map multiple libraries or
10 assemblies, of different multiplexed organisms, to a concatenated reference
11 containing one fused scaffold per organism. This will convert all of the
12 resulting stats files (one per library) to a single text file, with multiple
13 columns, indicating how much of the input hit the primary versus nonprimary
14 scaffolds.
15
16 If ingoresametaxa or ignoresamebarcode are used, ref names must be
17 in this format:
18 barcode,library,tax,location
19 For example:
20 6-G,N0296,gammaproteobacteria_bacterium,deep_ocean
21
22 Usage: summarizeseal.sh in=<file,file...> out=<file>
23
24 You can alternately run 'summarizeseal.sh *.txt out=out.txt'
25
26 Parameters:
27 in=<file> A list of stats files, or a text file containing one stats file name per line.
28 out=<file> Destination for summary.
29 printtotal=t (pt) Print a line summarizing the total contamination rate of all assemblies.
30 ignoresametaxa=f Ignore secondary hits sharing taxonomy.
31 ignoresamebarcode=f Ignore secondary hits sharing a barcode.
32 ignoresamelocation=f Ignore secondary hits sharing a sampling site.
33 totaldenominator=f (td) Use all bases as denominator rather than mapped bases.
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="-Xmx120m"
54 set=0
55
56 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
57 usage
58 exit
59 fi
60
61 calcXmx () {
62 source "$DIR""/calcmem.sh"
63 setEnvironment
64 parseXmx "$@"
65 }
66 calcXmx "$@"
67
68 summarizeseal() {
69 local CMD="java $EA $EOOM $z -cp $CP driver.SummarizeSealStats $@"
70 # echo $CMD >&2
71 eval $CMD
72 }
73
74 summarizeseal "$@"