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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 December 19, 2019
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7
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8 Description: Writes a shell script to download one genome assembly
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9 and gff per genus or species, from ncbi. Attempts to select the best assembly
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10 on the basis of contiguity.
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11
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12 Usage: fetchproks.sh <url> <outfile> <max species per genus: int> <use best: t/f>
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13
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14 Examples:
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15 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/bacteria/ bacteria.sh 2 true
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16 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/archaea/ archaea.sh 0 true
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17 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/viral/ viral.sh 0 true
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18 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/protozoa/ protozoa.sh 0 true
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19 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/invertebrate/ invertebrate.sh 0 true
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20 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/fungi/ fungi.sh 0 true
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21 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/plant/ plant.sh 0 true
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22 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/vertebrate_mammalian/ vertebrate_mammalian.sh 0 true
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23 fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/vertebrate_other/ vertebrate_other.sh 0 true
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24
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25 Mitochondrion, plasmid, and plastid are different and use gbff2gff.
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26
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27 Processing parameters:
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28 None yet!
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29
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30 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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31 "
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32 }
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33
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34 #This block allows symlinked shellscripts to correctly set classpath.
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35 pushd . > /dev/null
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36 DIR="${BASH_SOURCE[0]}"
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37 while [ -h "$DIR" ]; do
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38 cd "$(dirname "$DIR")"
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39 DIR="$(readlink "$(basename "$DIR")")"
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40 done
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41 cd "$(dirname "$DIR")"
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42 DIR="$(pwd)/"
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43 popd > /dev/null
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44
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45 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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46 CP="$DIR""current/"
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47
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48 z="-Xmx1g"
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49 z2="-Xms1g"
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50 set=0
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51
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52 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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53 usage
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54 exit
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55 fi
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56
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57 calcXmx () {
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58 source "$DIR""/calcmem.sh"
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59 setEnvironment
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60 parseXmx "$@"
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61 }
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62 calcXmx "$@"
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63
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64 fetchproks() {
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65 local CMD="java $EA $EOOM $z -cp $CP prok.FetchProks $@"
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66 echo $CMD >&2
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67 eval $CMD
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68 }
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69
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70 fetchproks "$@"
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