1#!/usr/local/bin/bash
2
3usage(){
4echo "
5Written by Brian Bushnell
6Last modified September 4, 2019
7
8Description:  Makes a representative set of taxa from all-to-all identity
9comparison.  Input should be in 3+ column TSV format (first 3 are required):
10(query, ref, ANI, qsize, rsize, qbases, rbases)
11...as produced by CompareSketch with format=3 and usetaxidname.
12Additional columns are allowed and will be ignored.
13
14Usage:  representative.sh in=<input file> out=<output file>
15
16Parameters:
17overwrite=f     (ow) Set to false to force the program to abort rather than
18                overwrite an existing file.
19threshold=0     Ignore edges under threshold value.  This also affects the
20                choice of centroids; a high threshold gives more weight to
21                higher-value edges.
22minratio=0      Ignores edges with a ratio below this value.
23invertratio=f   Invert the ratio when greater than 1.
24printheader=t   Print a header line in the output.
25printsize=t     Print the size of retained nodes.
26printclusters=t Print the nodes subsumed by each retained node.
27minsize=0       Ignore nodes under this size (in unique kmers).
28maxsize=0       If positive, ignore nodes over this size (unique kmers).
29minbases=0      Ignore nodes under this size (in total bases).
30maxbases=0      If positive, ignore nodes over this size (total bases).
31
32Taxonomy parameters:
33level=          Taxonomic level, such as phylum.  Filtering will operate on
34                sequences within the same taxonomic level as specified ids.
35                If not set, only matches to a node or its descendants will
36                be considered.
37ids=            Comma-delimited list of NCBI numeric IDs.  Can also be a
38                file with one taxID per line.
39names=          Alternately, a list of names (such as 'Homo sapiens').
40                Note that spaces need special handling.
41include=f       'f' will discard filtered sequences, 't' will keep them.
42tree=<file>     Specify a TaxTree file like tree.taxtree.gz.
43                On Genepool, use 'auto'.
44
45Java Parameters:
46-Xmx            This will set Java's memory usage, overriding autodetection.
47                -Xmx20g will
48                specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
49                The max is typically around 85% of physical memory.
50-eoom           This flag will cause the process to exit if an out-of-memory
51                exception occurs.  Requires Java 8u92+.
52-da             Disable assertions.
53
54Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
55"
56}
57
58#This block allows symlinked shellscripts to correctly set classpath.
59pushd . > /dev/null
60DIR="${BASH_SOURCE[0]}"
61while [ -h "$DIR" ]; do
62  cd "$(dirname "$DIR")"
63  DIR="$(readlink "$(basename "$DIR")")"
64done
65cd "$(dirname "$DIR")"
66DIR="$(pwd)/"
67popd > /dev/null
68
69#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
70CP="$DIR""current/"
71
72z="-Xmx4g"
73z2="-Xms4g"
74set=0
75
76if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
77	usage
78	exit
79fi
80
81calcXmx () {
82	source "$DIR""/calcmem.sh"
83	setEnvironment
84	parseXmx "$@"
85	if [[ $set == 1 ]]; then
86		return
87	fi
88	freeRam 4000m 84
89	z="-Xmx${RAM}m"
90	z2="-Xms${RAM}m"
91}
92calcXmx "$@"
93
94a_sample_mt() {
95	local CMD="java $EA $EOOM $z -cp $CP jgi.RepresentativeSet $@"
96	echo $CMD >&2
97	eval $CMD
98}
99
100a_sample_mt "$@"
101