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1 #!/bin/sh
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2 ##convert output of CAPS detection tool to GFF3
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3 ## usage
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4 # sh CAPS2gff.sh <input tabular CAPS output> <output file>
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5 #Copyright 2012 John McCallum
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6 #New Zealand Institute for Plant and Food Research
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7
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8 #This program is free software: you can redistribute it and/or modify
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9 # it under the terms of the GNU General Public License as published by
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10 # the Free Software Foundation, either version 3 of the License, or
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11 # (at your option) any later version.
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12 #
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13 # This program is distributed in the hope that it will be useful,
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14 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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15 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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16 # GNU General Public License for more details.
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17 #
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18 # You should have received a copy of the GNU General Public License
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19 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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20
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21 inputfile=$1
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22 outputfile=$2
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23 awk -F '\t' 'split($4,ID,":") {print ID[1], "FINDCAPS",ID[3],ID[4],ID[4],".",".",".","ID="$1";Enzyme="$5";Phase="$6}' $inputfile > $outputfile
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