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comparison heatmap_advanced.sh @ 6:1f13d304ddbd draft

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author insilico-bob
date Thu, 20 Jun 2019 11:36:53 -0400
parents 19382473a76b
children c5489978071a
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5:15c71ed09efa 6:1f13d304ddbd
1 #echo "1: " $1 1 #echo "1: " $1 " 2: " $2 " 3: " $3 " 4: " $4 " 5: " $5 " 6: " $6 " 7: " $7 " 8: " $8 " 9: " $9 " 10: " ${10}
2 #echo "2: " $2 2 #echo "11: " ${11} " 12: " ${12} 13: " ${13} 14: " ${14} " 15: " ${15} " 16: " ${16} " 17: " ${17} " 18: " ${18} " 19: " ${19} " 20: " ${20}
3 #echo "3: " $3 3 #echo "21: "${21}" 22: "${22}" 23: "${23}" 24: "${24}" 25: "${25}" 26: "${26}" 27: "${27}" 28: "${28}" 29: "${29}" 30: "${30}
4 #echo "4: " $4 4
5 #echo "5: " $5 5 #Count total number of parameters, dataLayer parameters, and classification parameters
6 #echo "6: " $6 6 parmSize=0
7 #echo "7: " $7 7 classSize=0
8 #echo "8: " $8 8 dataLayerSize=0
9 #echo "9: " $9 9 attribSize=0
10 #echo "10: " ${10} 10 for i in "$@"; do
11 #echo "11: " ${11} 11 currParm=$(cut -d'|' -f1 <<< $i)
12 #echo "12: " ${12} 12 parmSize=$((parmSize+1))
13 #echo "13: " ${13} 13 if [ $currParm = "classification" ]
14 #echo "14: " ${14} 14 then
15 #echo "15: " ${15} 15 classSize=$((classSize+1))
16 #echo "16: " ${16} 16 fi
17 #echo "17: " ${17} 17 if [ $currParm = "matrix_files" ]
18 #echo "18: " ${18} 18 then
19 #echo "19: " ${19} 19 dataLayerSize=$((dataLayerSize+1))
20 #echo "20: " ${20} 20 fi
21 #echo "21: " ${21} 21 if [ $currParm = "attribute" ]
22 #echo "22: " ${22} 22 then
23 #echo "23: " ${23} 23 attribSize=$((attribSize+1))
24 #echo "23: " ${24} 24 fi
25 #echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17} ${18} ${19} ${20} ${21} ${22} ${23} 25 done
26 26
27 #get tool data and tool install directories 27 if [ $dataLayerSize -lt 1 ]
28 tooldir=$(cut -d';' -f1 <<< ${12}) 28 then
29 tooldata=$(cut -d';' -f2 <<< ${12}) 29 noDataLayer="ERROR: No Heat Map Matrices provided. Please add at least one Heat Map Matrix to your request and try again."
30 30 echo $noDataLayer
31 exit $noDataLayer
32 fi
33
34 #Get tool data and tool install directories
35 tooldir=$1
36 tooldata=$2
31 #create temp directory for row and col order and dendro files. 37 #create temp directory for row and col order and dendro files.
32 tdir=$tooldata/$(date +%y%m%d%M%S) 38 tdir=$tooldata/$(date +%y%m%d%M%S)
33 echo $tdir
34 mkdir $tdir 39 mkdir $tdir
40 #echo "tdir: "$tdir
41
42 #Extract parameters for row and column order and dendro files
43 rowOrderFile=$tdir/ROfile.txt
44 rowDendroFile=$tdir/RDfile.txt
45 colOrderFile=$tdir/COfile.txt
46 colDendroFile=$tdir/CDfile.txt
47 rowOrderJson='"order_file": "'$rowOrderFile'",'
48 rowDendroJson='"dendro_file": "'$rowDendroFile'",'
49 colOrderJson='"order_file": "'$colOrderFile'",'
50 colDendroJson='"dendro_file": "'$colDendroFile'",'
51
52 #BEGIN: Construct JSON for all non-repeating parameters
53 parmJson='{'
54 rowConfigJson='"row_configuration": {'
55 colConfigJson='"col_configuration": {'
56
57 ctr=0
58 for i in "$@"; do
59 if [ $ctr -gt 1 ]
60 then
61 currParm=$(cut -d'|' -f1 <<< $i)
62 if [ $currParm != "matrix_files" ] && [ $currParm != "row_configuration" ] && [ $currParm != "col_configuration" ] && [ $currParm != "classification" ] && [ $currParm != "attribute" ]
63 then
64 #Parse pipe-delimited parameter parameter
65 parmJson=$parmJson' "'$(cut -d'|' -f1 <<< $i)'":"'$(cut -d'|' -f2 <<< $i)'",'
66 fi
67 if [ $currParm = "row_configuration" ]
68 then
69 rowOrder=$(cut -d'|' -f3 <<< $i)
70 rowDistance=$(cut -d'|' -f5 <<< $i)
71 rowAgglomeration=$(cut -d'|' -f7 <<< $i)
72 rowCuts=$(cut -d'|' -f9 <<< $i)
73 rowLabels=$(cut -d'|' -f11 <<< $i)
74 rowDataTypeJson='"'$(cut -d'|' -f10 <<< $i)'":["'$rowLabels'"],'
75 rowCutType=$(cut -d'|' -f16 <<< $i)
76 rowTopItemsJson=''
77 rowTopItems=$(cut -d'|' -f13 <<< $i)
78 if [ $rowTopItems != "None" ] && [ $rowTopItems != "" ]
79 then
80 rowTopItemsJson='"'$(cut -d'|' -f12 <<< $i)'": ['
81 rowTopItems=${rowTopItems//,/'","'}
82 rowTopItemsJson=$rowTopItemsJson'"'$rowTopItems'"],'
83 fi
84 rowCutsJson=''
85 if [ $rowCutType != "none" ]
86 then
87 cutValues=$(cut -d'|' -f15 <<< $i)
88 if [ $cutValues != "None" ] && [ $cutValues != "0" ]
89 then
90 if [ $rowCutType = "treecuts" ]
91 then
92 rowCutsJson=$rowCutsJson'"tree_cuts": "'$cutValues'",'
93 rowCutsJson=$rowCutsJson'"cut_width": "5",'
94 fi
95 if [ $rowCutType = "positional" ]
96 then
97 rowCutErrorVal=0
98 [[ $cutValues != ?(-)+([0-9,]) ]] && rowCutErrorVal=$((rowCutErrorVal+1))
99 if [ $rowCutErrorVal -gt 0 ]
100 then
101 echo "GALAXY PARAMETER WARNING: Non-numeric values found for Row Fixed Gap Locations. Ignoring parameter value: "$cutValues
102 else
103 rowCutsJson=$rowCutsJson'"cut_locations": ['$cutValues'],'
104 rowCutsJson=$rowCutsJson'"cut_width": "5",'
105 fi
106 fi
107 fi
108 fi
109 rowConfigJson=$rowConfigJson$rowDataTypeJson$rowCutsJson$rowTopItemsJson
110 if [ $rowOrder = 'Hierarchical' ]
111 then
112 rowConfigJson=$rowConfigJson$rowOrderJson$rowDendroJson
113 fi
114 rowConfigJson=$rowConfigJson' "'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f6 <<< $i)'":"'$(cut -d'|' -f7 <<< $i)'","'$(cut -d'|' -f17 <<< $i)'":"'$(cut -d'|' -f18 <<< $i)'","'$(cut -d'|' -f19 <<< $i)'":"'$(cut -d'|' -f20 <<< $i)'"},'
115 fi
116 if [ $currParm = "col_configuration" ]
117 then
118 colOrder=$(cut -d'|' -f3 <<< $i)
119 colDistance=$(cut -d'|' -f5 <<< $i)
120 colAgglomeration=$(cut -d'|' -f7 <<< $i)
121 colCuts=$(cut -d'|' -f9 <<< $i)
122 colLabels=$(cut -d'|' -f11 <<< $i)
123 colDataTypeJson='"'$(cut -d'|' -f10 <<< $i)'":["'$colLabels'"],'
124 colCutType=$(cut -d'|' -f16 <<< $i)
125 colTopItemsJson=''
126 colTopItems=$(cut -d'|' -f13 <<< $i)
127 if [ $colTopItems != "None" ] && [ $colTopItems != "" ]
128 then
129 colTopItemsJson='"'$(cut -d'|' -f12 <<< $i)'": ['
130 colTopItems=${colTopItems//,/'","'}
131 colTopItemsJson=$colTopItemsJson'"'$colTopItems'"],'
132 fi
133 colCutsJson=''
134 if [ $colCutType != "none" ]
135 then
136 cutValues=$(cut -d'|' -f15 <<< $i)
137 if [ $cutValues != "None" ] && [ $cutValues != "0" ]
138 then
139 if [ $colCutType = "treecuts" ]
140 then
141 colCutsJson=$colCutsJson'"tree_cuts": "'$cutValues'",'
142 colCutsJson=$colCutsJson'"cut_width": "5",'
143 fi
144 if [ $colCutType = "positional" ]
145 then
146 colCutErrorVal=0
147 [[ $cutValues != ?(-)+([0-9,]) ]] && colCutErrorVal=$((colCutErrorVal+1))
148 if [ $colCutErrorVal -gt 0 ]
149 then
150 echo "GALAXY PARAMETER WARNING: Non-numeric values found for Column Fixed Gap Locations. Ignoring parameter value: "$cutValues
151 else
152 colCutsJson=$colCutsJson'"cut_locations": ['$cutValues'],'
153 colCutsJson=$colCutsJson'"cut_width": "5",'
154 fi
155 fi
156 fi
157 fi
158 colConfigJson=$colConfigJson$colDataTypeJson$colCutsJson$colTopItemsJson
159 if [ $colOrder = 'Hierarchical' ]
160 then
161 colConfigJson=$colConfigJson$colOrderJson$colDendroJson
162 fi
163 colConfigJson=$colConfigJson' "'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f6 <<< $i)'":"'$(cut -d'|' -f7 <<< $i)'","'$(cut -d'|' -f17 <<< $i)'":"'$(cut -d'|' -f18 <<< $i)'","'$(cut -d'|' -f19 <<< $i)'":"'$(cut -d'|' -f20 <<< $i)'"},'
164 fi
165 fi
166 ctr=$((ctr+1))
167 done
168
169 #END: Construct JSON for all non-repeating parameters
170 #echo "rowOrder: "$rowOrder
171 #echo "rowDistance: "$rowDistance
172 #echo "rowAgglomeration: "$rowAgglomeration
173 #echo "rowCuts: "$rowCuts
174 #echo "rowLabels: "$rowLabels
175 #echo "ROW CONFIG JSON: "$rowConfigJson
176 #echo "colOrder: "$colOrder
177 #echo "colDistance: "$colDistance
178 #echo "colAgglomeration: "$colAgglomeration
179 #echo "colCuts: "$colCuts
180 #echo "colLabels: "$colLabels
181 #echo "COL CONFIG JSON: "$colConfigJson
182
183 #BEGIN: Construct JSON for data layers
184 matrixJson='"matrix_files": [ '
185 inputMatrix=''
186 dataLayerIter=0
187 dataLayerNames=''
188 for i in "$@"; do
189 currParm=$(cut -d'|' -f1 <<< $i)
190 if [ $currParm = "matrix_files" ]
191 then
192 if [ $dataLayerIter -lt 1 ]
193 then
194 inputMatrix=$(cut -d'|' -f3 <<< $i)
195 fi
196 currMatrixName=$(cut -d'|' -f5 <<< $i)
197 dataLayerIter=$((dataLayerIter+1))
198 if [[ $dataLayerNames =~ $currMatrixName ]]
199 then
200 currMatrixName=$currMatrixName$dataLayerIter
201 fi
202 dataLayerNames=$dataLayerNames$currMatrixName
203 colorPref=$(cut -d'|' -f16 <<< $i)
204 colorMapJson=''
205 if [ $colorPref = "defined" ]
206 then
207 #validations to place leading zero on first breakpoint (if necessary)
208 b1=$(cut -d'|' -f20 <<< $i)
209 b1first=$(cut -d'.' -f1 <<< $b1)
210 if [ $b1first = "-" ]
211 then
212 b1="-0."$(cut -d'.' -f2 <<< $b1)
213 fi
214 if [ "$b1first" = "" ]
215 then
216 b1="0"$b1
217 fi
218 #validations to place leading zero on second breakpoint (if necessary)
219 b2=$(cut -d'|' -f21 <<< $i)
220 b2first=$(cut -d'.' -f1 <<< $b2)
221 if [ $b2first = "-" ]
222 then
223 b2="-0."$(cut -d'.' -f2 <<< $b2)
224 fi
225 if [ "$b2first" = "" ]
226 then
227 b2="0"$b2
228 fi
229 #validations to place leading zero on third breakpoint (if necessary)
230 b3=$(cut -d'|' -f22 <<< $i)
231 b3first=$(cut -d'.' -f1 <<< $b3)
232 if [ $b3first = "-" ]
233 then
234 b3="-0."$(cut -d'.' -f2 <<< $b3)
235 fi
236 if [ "$b3first" = "" ]
237 then
238 b3="0"$b3
239 fi
240 #validation to ensure that all entered breakpoints are numeric values
241 regExp='^[+-]?([0-9]+\.?|[0-9]*\.[0-9]+)$'
242 if [[ $b1 =~ $regExp ]] && [[ $b2 =~ $regExp ]] && [[ $b3 =~ $regExp ]]
243 then
244 colorMapJson=$colorMapJson'"color_map": {"colors": ["'$(cut -d'|' -f17 <<< $i)'","'$(cut -d'|' -f18 <<< $i)'","'$(cut -d'|' -f19 <<< $i)'"],'
245 colorMapJson=$colorMapJson'"thresholds": ['$b1','$b2','$b3'],'
246 colorMapJson=$colorMapJson'"missing":"'$(cut -d'|' -f23 <<< $i)'"},'
247 else
248 echo "GALAXY PARAMETER WARNING: Not all user-defined breakpoints are numbers. Defined breakpoints and colors will be ignored."
249 fi
250 fi
251 #Parse pipe-delimited parameter parameter
252 matrixJson=$matrixJson' {'$colorMapJson'"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$currMatrixName'","'$(cut -d'|' -f6 <<< $i)'":"'$(cut -d'|' -f7 <<< $i)'","'$(cut -d'|' -f8 <<< $i)'":"'$(cut -d'|' -f9 <<< $i)'","'$(cut -d'|' -f10 <<< $i)'":"'$(cut -d'|' -f11 <<< $i)'","'$(cut -d'|' -f12 <<< $i)'":"'$(cut -d'|' -f13 <<< $i)'","'$(cut -d'|' -f14 <<< $i)'":"'$(cut -d'|' -f15 <<< $i)'"}'
253 if [ $dataLayerIter -lt $dataLayerSize ]
254 then
255 matrixJson=$matrixJson','
256 fi
257 fi
258 done
259 matrixJson=$matrixJson"],"
260 #END: Construct JSON for data layers
261 #echo "DATA LAYER JSON: "$matrixJson
262 #echo "INPUT MATRIX: "$inputMatrix
263
264 #BEGIN: Construct JSON for attributes
265 attribJson='"chm_attributes": [ '
266 attribIter=0
267 for i in "$@"; do
268 currParm=$(cut -d'|' -f1 <<< $i)
269 if [ $currParm = "attribute" ]
270 then
271 attribIter=$((attribIter+1))
272 attribParam=$(cut -d'|' -f2 <<< $i)
273 #Parse pipe-delimited 2-part data layer parameter
274 attribJson=$attribJson' {"'$(cut -d':' -f1 <<< $attribParam)'":"'$(cut -d':' -f2 <<< $attribParam)'"}'
275 if [ $attribIter -lt $attribSize ]
276 then
277 attribJson=$attribJson','
278 fi
279 fi
280 done
281 attribJson=$attribJson'],'
282 #END: Construct JSON for attributes
283 #echo "ATTRIB JSON: "$attribJson
284
285 #BEGIN: Construct JSON for classification files
286 classJson='"classification_files": [ '
287 colCutClass=''
288 rowCutClass=''
289 if [ $rowCuts -gt 1 ]
290 then
291 rowCutClass='{"name": "Class", "path": "'$tdir'/ROfile.txt.cut","position": "row", "color_map": {"type": "discrete"}, "bar_type": "color_plot"}'
292 fi
293
294 if [ $colCuts -gt 1 ]
295 then
296 if [ $rowCuts -gt 1 ]
297 then
298 rowCutClass=$rowCutClass','
299 fi
300 colCutClass='{"name": "Class", "path": "'$tdir'/COfile.txt.cut","position": "column", "color_map": {"type": "discrete"}, "bar_type": "color_plot"}'
301 if [ $classSize -gt 0 ]
302 then
303 colCutClass=$colCutClass','
304 fi
305 else
306 if [ $rowCuts -gt 1 ] && [ $classSize -gt 0 ]
307 then
308 rowCutClass=$rowCutClass','
309 fi
310 fi
311
312 classJson=$classJson$rowCutClass$colCutClass
313 classIter=0
314 for i in "$@"; do
315 currParm=$(cut -d'|' -f1 <<< $i)
316 if [ $currParm = "classification" ]
317 then
318 classIter=$((classIter+1))
319 className=$(cut -d'|' -f3 <<< $i)
320 #Parse pipe-delimited 3-part classification bar parameter
321 classJson=$classJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f8 <<< $i)'":"'$(cut -d'|' -f9 <<< $i)'","'$(cut -d'|' -f12 <<< $i)'":"'$(cut -d'|' -f13 <<< $i)'","'$(cut -d'|' -f14 <<< $i)'":"'$(cut -d'|' -f15 <<< $i)'"'
322 classCat=$(cut -d'|' -f7 <<< $i)
323 classColorType=$(cut -d'_' -f2 <<< $classCat)
324 classJson=$classJson','
325 classHeight=$(cut -d'|' -f11 <<< $i)
326 heightErrorVal=0
327 [[ $classHeight != ?(-)+([0-9]) ]] && heightErrorVal=$((heightErrorVal+1))
328 if [ $heightErrorVal -gt 0 ]
329 then
330 echo 'GALAXY PARAMETER WARNING: Non-numeric values found for covariate bar ('$className') height. Height value ignored and default of 15 used: '$classHeight
331 else
332 classJson=$classJson'"height": "'$classHeight'",'
333 fi
334 classJson=$classJson' "position":"'$(cut -d'_' -f1 <<< $classCat)'","color_map": {"type":"'$classColorType'"}}'
335 if [ $classIter -lt $classSize ]
336 then
337 classJson=$classJson','
338 fi
339 fi
340 done
341 classJson=$classJson']'
342 #END: Construct JSON for classification files
343 #echo "CLASSIFICATION JSON: "$classJson
344
345 #Complete construction of Parameter JSON file by adding all JSON sections created above
346 parmJson=$parmJson$rowConfigJson$colConfigJson$attribJson$matrixJson$classJson
347 parmJson=$parmJson'}'
348 #echo "COMPLETED PARAMETER JSON: "$parmJson
349
35 #run R to cluster matrix 350 #run R to cluster matrix
36 output="$(R --slave --vanilla --file=$tooldir/CHM_Advanced.R --args $4 $5 $6 $7 $8 $9 ${10} $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt ${13} ${14} ${15} ${16} 2>&1)" 351 output="$(R --slave --vanilla --file=$tooldir/CHM_Advanced.R --args $inputMatrix $rowOrder $rowDistance $rowAgglomeration $colOrder $colDistance $colAgglomeration $rowOrderFile $colOrderFile $rowDendroFile $colDendroFile $rowCuts $colCuts $rowLabels $colLabels 2>&1)"
352 # Check for errors from R step, log them if found, and exit script
37 rc=$?; 353 rc=$?;
38 if [ $rc != 0 ] 354 if [ $rc != 0 ]
39 then 355 then
40 echo $output; 356 echo $output;
41 if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ] 357 if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ]
42 then 358 then
43 echo ""; 359 echo "";
44 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."; 360 echo "NOTE 1: This error can occur when a covariate file has inadvertently been selected as an Input Matrix. Check your Input Matrix entry.";
45 echo "This error may also be caused when a covariate file has inadvertently been selected as an Input Matrix. Check your Input Matrix entry."; 361 echo "NOTE 2: This error can occur when there is no variation in a data rows or columns in the input matrix. Try a different distance measure or remove rows/columns without variation.";
46 fi 362 fi
47 exit $rc; 363 exit $rc;
48 fi 364 fi
49 365
50 #there are a variable number of triplicate parameters for classification bars 366 #Call java program to generate NGCHM viewer files.
51 count=0 367 java -jar $tooldir/GalaxyMapGen.jar "$parmJson"
52 classifications=''
53
54 #if row cut was done, add that autogenerated classification
55 if [ ${13} -gt 1 ]
56 then
57 classifications="Class $tdir/ROfile.txt.cut row_categorical color_plot"
58 fi
59
60 #if col cut was done, add that autogenerated classification
61 if [ ${14} -gt 1 ]
62 then
63 classifications="$classifications Class $tdir/COfile.txt.cut col_categorical color_plot"
64 fi
65
66 #now add the user provided classification files
67 for i in "$@"; do
68 if [ $count -gt 20 ]
69 then
70 # echo "class entry: " $i
71 classifications=$classifications' '$i
72 fi
73 count=$((count+1))
74 done
75 #echo "classifications: " $classifications
76
77 #call java program to generate NGCHM viewer files.
78 java -jar $tooldir/GalaxyMapGen.jar "${1}" "${2}" "${3}" DataLayer1 $4 linear ${15} ${16} $5 $6 $7 $tdir/ROfile.txt $tdir/RDfile.txt "${17}" "${19}" $8 $9 ${10} $tdir/COfile.txt $tdir/CDfile.txt "${18}" "${20}" ${11} "${21}" $classifications
79 #clean up tempdir 368 #clean up tempdir
80 rm -rf $tdir 369 rm -rf $tdir