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2
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1 echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17}
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32
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2
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3 #run python to validate the input matrix and covariate files (if any)
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4 #output="$(python ${11}/mda_heatmap_gen.py $@)"
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5 output=$(python ${11}/mda_heatmap_gen.py "$@")
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6 rc=$?;
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7 echo $output;
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8 if [ $rc != 0 ]
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9 then
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10 exit $rc;
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11 fi
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12
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13
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2
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14 #create temp directory for row and col order and dendro files.
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15 tdir=${11}/$(date +%y%m%d%M%S)
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16 echo $tdir
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17 mkdir $tdir
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32
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18
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2
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19 #run R to cluster matrix
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20 output="$(R --slave --vanilla --file=${11}/CHM.R --args $3 $4 $5 $6 $7 $8 $9 $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt ${12} ${13} ${14} ${15} 2>&1)"
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21 rc=$?;
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22 if [ $rc != 0 ]
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23 then
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24 echo $output;
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25 if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ]
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26 then
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27 echo "";
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28 echo "Note: This error can occur when there is no variation in a row or column. Try a different distance measure or remove rows/columns without variation.";
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29 fi
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30 exit $rc;
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31 fi
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32
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33 #there are a variable number of triplicate parameters for classification bars
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34 count=0
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35 classifications=''
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36
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37 #if row cut was done, add that autogenerated classification
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38 if [ ${12} -gt 1 ]
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39 then
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40 classifications="Class $tdir/ROfile.txt.cut row_categorical"
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41 fi
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42
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43 #if col cut was done, add that autogenerated classification
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44 if [ ${13} -gt 1 ]
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45 then
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46 classifications="$classifications Class $tdir/COfile.txt.cut col_categorical"
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47 fi
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48
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49 #now add the user provided classification files
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50 for i in "$@"; do
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51 if [ $count -gt 14 ]
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52 then
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53 classifications=$classifications' '$i
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54 fi
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55 count=$((count+1))
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56 done
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57 #call java program to generate NGCHM viewer files.
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58 java -jar ${11}/GalaxyMapGen.jar "${1}" "${2}" DataLayer1 $3 linear ${14} ${15} $4 $5 $6 $tdir/ROfile.txt $tdir/RDfile.txt $7 $8 $9 $tdir/COfile.txt $tdir/CDfile.txt ${10} $classifications
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59 #clean up tempdir
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60 rm -rf $tdir
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