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3
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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 filein=$1
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6 fileout_label=$(date "+%Y%m%d%H%M%S")
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7 step=$2
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8 window=$3
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9 filelog=$4
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10 fileout_taj=$5
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11 fileout_tstv=$6
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12 fileout_windowed=$7
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13 fileout_snp=$8
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14 group=$9
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15 if [ "$group" != "none" ]
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16 then fileout_fst=${10}
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17 fileout_fst_marker=${11}
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18 fileout_taj_combined=${12}
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19 fileout_windowed_combined=${13}
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20 fi
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21
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22
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23 cp $filein ${filein}.vcf
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24 if [ "$group" != "none" ]
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25 then perl $tool_path/VCFToolsSlidingWindow.pl --input ${filein}.vcf --out $fileout_label --step $step --window $window --group $group
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26 else perl $tool_path/VCFToolsSlidingWindow.pl --input ${filein}.vcf --out $fileout_label --step $step --window $window
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27 fi
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28
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29 mv ${fileout_label}.vcftools.log $filelog
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30 mv ${fileout_label}.Tajima.D ${fileout_taj}
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31 mv ${fileout_label}.TsTv ${fileout_tstv}
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32 mv ${fileout_label}.windowed.pi ${fileout_windowed}
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33 mv ${fileout_label}.snpden ${fileout_snp}
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34
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35 if [ "$group" != "none" ]
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36 then mv ${fileout_label}.fst.txt ${fileout_fst}
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37 mv ${fileout_label}.fst.by_marker.genes.txt ${fileout_fst_marker}
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38 mv ${fileout_label}.combined.dtajima.txt ${fileout_taj_combined}
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39 mv ${fileout_label}.combined.pi.txt ${fileout_windowed_combined}
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40 fi
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41
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42 rm -f ${filein}.vcf ${filein}.vcf.*
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43
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