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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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4
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7 window=$2
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8 filelog=$3
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9 fileout_taj=$4
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10 fileout_tstv=$5
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11 fileout_windowed=$6
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12 fileout_snp=$7
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13 group=$8
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3
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14 if [ "$group" != "none" ]
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4
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15 then fileout_fst=${9}
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16 fileout_fst_marker=${10}
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17 fileout_taj_combined=${11}
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18 fileout_windowed_combined=${12}
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7
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19 fileout_tstv_combined=${13}
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20 fileout_snp_combined=${14}
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3
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21 fi
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22
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23
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24 cp $filein ${filein}.vcf
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25 if [ "$group" != "none" ]
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8
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26 then
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27 if [ $(sort -k2,2 -t ';' -u $group | cut -f2 -d ';' |wc -l) -ge 3 ]
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28 then
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29 echo 'ERROR: it only works with 2 groups. There is too many groups in your file.' >&2
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30 exit 1
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31 else
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32 perl $tool_path/VCFToolsSlidingWindow.pl --input ${filein}.vcf --out $fileout_label --window $window --group $group
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33 fi
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34
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35
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4
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36 else perl $tool_path/VCFToolsSlidingWindow.pl --input ${filein}.vcf --out $fileout_label --window $window
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3
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37 fi
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38
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39 mv ${fileout_label}.vcftools.log $filelog
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40 mv ${fileout_label}.Tajima.D ${fileout_taj}
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41 mv ${fileout_label}.TsTv ${fileout_tstv}
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42 mv ${fileout_label}.windowed.pi ${fileout_windowed}
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43 mv ${fileout_label}.snpden ${fileout_snp}
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44
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45 if [ "$group" != "none" ]
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46 then mv ${fileout_label}.fst.txt ${fileout_fst}
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47 mv ${fileout_label}.fst.by_marker.genes.txt ${fileout_fst_marker}
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48 mv ${fileout_label}.combined.dtajima.txt ${fileout_taj_combined}
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49 mv ${fileout_label}.combined.pi.txt ${fileout_windowed_combined}
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7
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50 paste ${fileout_label}.Pop1.TsTv ${fileout_label}.Pop2.TsTv | column -s $'\t' -t | awk '{OFS="\t"; print $1,$2,$4,$8} ' | awk 'NR==1{$3="Pop1";$4="Pop2"}1' > ${fileout_tstv_combined}
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51 paste ${fileout_label}.Pop1.snpden ${fileout_label}.Pop2.snpden | column -s $'\t' -t | awk '{OFS="\t"; print $1,$2,$4,$8} ' | awk 'NR==1{$3="Pop1";$4="Pop2"}1' > ${fileout_snp_combined}
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3
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52 fi
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53
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54 rm -f ${filein}.vcf ${filein}.vcf.*
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55
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