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9
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1 #!/bin/bash
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2
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3 tool_path=$(dirname $0)
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4
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5
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6
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7 filein=$1
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8 fileout_label=$(date "+%Y%m%d%H%M%S")
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9 fileout=$2
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10 option=$3
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11
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12 option_text=''
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13
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14
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15 if [ "$option" != "none" ]
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16 then fileout_seq=$4
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17 fileout_fa1=$5
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18 filefasta=$6
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19 if [ "$option" == "fasta_gff" ]
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20 then filegff=$7
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21 fi
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22 fi
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23
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24 if [ "$option" == "fasta" ]
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25 then option_text="--reference $filefasta"
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26 fi
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27
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28 if [ "$option" == "fasta_gff" ]
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29 then option_text="--reference $filefasta --gff $filegff"
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30 fi
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31
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32
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33 perl $tool_path/VCF2FastaAndHapmap.pl --vcf $filein --out $fileout_label $option_text
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34
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35
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36 cp $fileout_label.hapmap $fileout ; rm $fileout_label.hapmap
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37
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38 if [ "$option" == "fasta_gff" ]
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39 then cp $fileout_label.flanking.txt $fileout_seq ; rm $fileout_label.flanking.txt ; cp $fileout_label.gene_alignment.fas $fileout_fa1 ; rm $fileout_label.gene_alignment.fas ;
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40 fi
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41
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42 if [ "$option" == "fasta" ]
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43 then cp $fileout_label.flanking.txt $fileout_seq ; rm $fileout_label.flanking.txt ;
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44 fi
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45
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