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1 #!/bin/bash
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2 dir="$(cd "$(dirname "$0")" && pwd)"
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3
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4 testID=$1
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5 species=$2
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6 substitutionModel=$3
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7 mutabilityModel=$4
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8 clonal=$5
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9 fixIndels=$6
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10 region=$7
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11 input=$8
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12 outDir=$9
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13 #mkdir $outDir
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14 outID=${10}
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15 outFile=${11}
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16 outFile2=${12}
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17
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18 cd $dir
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19 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $input $dir/ $outID 2> /dev/null
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20
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21 mv $dir/${outID}.txt $outFile
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22 mv $dir/${outID}.RData $outFile2
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23
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24 #tail -n+2 $outDir/${outID}.txt > $outDir/tmp.txt
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25 #echo "<html><table border='1'><thead>" >> $outFile
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26 #echo "<tr><th>Type</th><th>ID</th><th>Observed_CDR_R</th><th>Observed_CDR_S</th><th>Observed_FWR_R</th><th>Observed_FWR_S</th><th>Expected_CDR_R</th><th>Expected_CDR_S</th><th>Expected_FWR_R</th><th>Expected_FWR_S</th><th>Focused_Sigma_CDR</th><th>Focused_CIlower_CDR</th><th>Focused_CIupper_CDR</th><th>Focused_Sigma_FWR</th><th>Focused_CIlower_FWR</th><th>Focused_CIupper_FWR</th><th>Focused_P_CDR</th><th>Focused_P_FWR</th></tr></thead><tbody>" >> $outFile
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27 #while read Type ID Observed_CDR_R Observed_CDR_S Observed_FWR_R Observed_FWR_S Expected_CDR_R Expected_CDR_S Expected_FWR_R Expected_FWR_S Focused_Sigma_CDR Focused_CIlower_CDR Focused_CIupper_CDR Focused_Sigma_FWR Focused_CIlower_FWR Focused_CIupper_FWR Focused_P_CDR Focused_P_FWR
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28 #do
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29 # echo "<tr><td>$Type</td><td>$ID</td><td>$Observed_CDR_R</td><td>$Observed_CDR_S</td><td>$Observed_FWR_R</td><td>$Observed_FWR_S</td><td>$Expected_CDR_R</td><td>$Expected_CDR_S</td><td>$Expected_FWR_R</td><td>$Expected_FWR_S</td><td>$Focused_Sigma_CDR</td><td>$Focused_CIlower_CDR</td><td>$Focused_CIupper_CDR</td><td>$Focused_Sigma_FWR</td><td>$Focused_CIlower_FWR</td><td>$Focused_CIupper_FWR</td><td>$Focused_P_CDR</td><td>$Focused_P_FWR</td></tr>" >> $outFile
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30 #done < $outDir/tmp.txt
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31 #echo "</tbody></table></html>" >> $outFile
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32 #rm $outDir/tmp.txt
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33
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