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jpayne@69
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1 #!/bin/bash
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2
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3 usage(){
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4 echo "
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5 Written by Brian Bushnell
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6 Last modified April 24, 2019
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7
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8 Description: Reformats a fungal assembly for release.
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9 Also creates contig and agp files.
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10
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11 Usage: fungalrelease.sh in=<input file> out=<output file>
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12
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13 I/O parameters:
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14 in=<file> Input scaffolds.
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15 out=<file> Output scaffolds.
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16 outc=<file> Output contigs.
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17 qfin=<file> Optional quality scores input.
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18 qfout=<file> Optional quality scores output.
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19 qfoutc=<file> Optional contig quality scores output.
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20 agp=<file> Output AGP file.
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21 legend=<file> Output name legend file.
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22 overwrite=f (ow) Set to false to force the program to abort rather than
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23 overwrite an existing file.
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24
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25 Processing parameters:
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26 fastawrap=60 Wrap length for fasta lines.
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27 tuc=t Convert sequence to upper case.
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28 baniupac=t Crash on encountering a non-ACGTN base call.
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29 mingap=10 Expand all gaps (Ns) to be at least this long.
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30 mingapin=1 Only expand gaps that are at least this long.
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31 sortcscaffolds=t Sort scaffolds descending by length.
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32 sortcontigs=f Sort contigs descending by length.
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33 renamescaffolds=t Rename scaffolds to 'scaffold_#'.
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34 scafnum=1 Number of first scaffold.
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35 renamecontigs=f Rename contigs to 'contig_#' instead of 'scafname_c#'.
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36 contignum=1 Number of first contig; only used if renamecontigs=t.
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37 minscaf=1 Only retain scaffolds at least this long.
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38 mincontig=1 Only retain contigs at least this long.
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39
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40 Java Parameters:
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41 -Xmx This will set Java's memory usage, overriding autodetection.
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42 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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43 The max is typically 85% of physical memory.
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44 -eoom This flag will cause the process to exit if an
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45 out-of-memory exception occurs. Requires Java 8u92+.
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46 -da Disable assertions.
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47
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48 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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49 "
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50 }
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51
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52 #This block allows symlinked shellscripts to correctly set classpath.
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53 pushd . > /dev/null
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54 DIR="${BASH_SOURCE[0]}"
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55 while [ -h "$DIR" ]; do
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56 cd "$(dirname "$DIR")"
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57 DIR="$(readlink "$(basename "$DIR")")"
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58 done
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59 cd "$(dirname "$DIR")"
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60 DIR="$(pwd)/"
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61 popd > /dev/null
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62
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63 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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64 CP="$DIR""current/"
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65
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66 z="-Xmx4g"
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67 z2="-Xms4g"
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68 set=0
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69
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70 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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71 usage
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72 exit
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73 fi
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74
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75 calcXmx () {
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76 source "$DIR""/calcmem.sh"
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77 setEnvironment
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78 parseXmx "$@"
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79 if [[ $set == 1 ]]; then
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80 return
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81 fi
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82 }
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83 calcXmx "$@"
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84
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85 fungalrelease() {
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86 local CMD="java $EOOM $EA $EOOM $z $z2 -cp $CP jgi.FungalRelease $@"
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87 echo $CMD >&2
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88 eval $CMD
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89 }
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90
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91 fungalrelease "$@"
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