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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/mergeribo.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 January 28, 2020
7
8 Description: Merges files of SSU sequences to keep one per taxID.
9 By default, a consensus is generated per TaxID, then the sequence
10 best matching that consensus is used:
11 First, all sequences per TaxID are aligned to a reference consensus.
12 Second, the best-matching sequence is used as a seed, and all other
13 sequences for that TaxID are aligned to the seed to generate a new consensus.
14 Third, in 'consensus' mode, that consensus is simply output.
15 In 'best' mode (default), all sequences are aligned again to the new consensus,
16 and the best-matching is output.
17
18 Usage: mergeribo.sh in=<file,file> out=<file> 16S
19
20 Standard parameters:
21 in=<file,file> Comma-delimited list of files.
22 out=<file> Output file.
23 out2=<file> Read 2 output if reads are in two files.
24 overwrite=f (ow) Set to false to force the program to abort rather than
25 overwrite an existing file.
26 showspeed=t (ss) Set to 'f' to suppress display of processing speed.
27 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
28 level; lower compression is faster.
29
30 Processing parameters:
31 alt=<file> Lower priority data. Only used if there is no SSU associated
32 with the TaxID from the primary input.
33 best=t Output the best representative per taxID.
34 consensus=f Output a consensus per taxID instead of the best input
35 sequence. Mutually exclusive with best.
36 fast=f Output the best sequence based on alignment to global consensus
37 (the seed) rather than individual consensus.
38 minid=0.62 Ignore sequences with identity lower than this to the global
39 consensus.
40 maxns=-1 Ignore sequences with more than this many Ns, if non-negative.
41 minlen=1 Ignore sequences shorter than this.
42 maxlen=4000 Ignore sequences longer than this.
43 16S=t Align to 16S consensus to pick the seed. Mutually exclusive.
44 18S=f Align to 18S consensus to pick the seed. Mutually exclusive.
45
46 Java Parameters:
47 -Xmx This will set Java's memory usage, overriding autodetection.
48 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
49 specify 200 megs. The max is typically 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
54 Please 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.
59 pushd . > /dev/null
60 DIR="${BASH_SOURCE[0]}"
61 while [ -h "$DIR" ]; do
62 cd "$(dirname "$DIR")"
63 DIR="$(readlink "$(basename "$DIR")")"
64 done
65 cd "$(dirname "$DIR")"
66 DIR="$(pwd)/"
67 popd > /dev/null
68
69 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
70 CP="$DIR""current/"
71
72 z="-Xmx4g"
73 z2="-Xms4g"
74 set=0
75
76 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
77 usage
78 exit
79 fi
80
81 calcXmx () {
82 source "$DIR""/calcmem.sh"
83 setEnvironment
84 parseXmx "$@"
85 if [[ $set == 1 ]]; then
86 return
87 fi
88 freeRam 4000m 42
89 z="-Xmx${RAM}m"
90 z2="-Xms${RAM}m"
91 }
92 calcXmx "$@"
93
94 mergeribo() {
95 local CMD="java $EA $EOOM $z -cp $CP prok.MergeRibo $@"
96 echo $CMD >&2
97 eval $CMD
98 }
99
100 mergeribo "$@"