Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 35:d7580295e13b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Fri, 22 Jan 2016 08:45:29 -0500
parents f2010de70741
children a2fdcf1a2e50
comparison
equal deleted inserted replaced
34:f2010de70741 35:d7580295e13b
49 echo "productive_counting.txt" 49 echo "productive_counting.txt"
50 echo "<html><head><title>Report on:" >> $outputFile 50 echo "<html><head><title>Report on:" >> $outputFile
51 51
52 mkdir $outputDir/circos 52 mkdir $outputDir/circos
53 cp $dir/circos/* $outputDir/circos/ 53 cp $dir/circos/* $outputDir/circos/
54 for sample in $samples; do 54 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf
55 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output
55 echo " $sample" >> $outputFile 56 echo " $sample" >> $outputFile
56 57
58 circos_file="$outputDir/${sample}_VJ_circos.txt"
59 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
60 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
61 /home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1
62 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png
63
64
65 if [[ "$useD" == "true" ]] ; then
57 circos_file="$outputDir/${sample}_VD_circos.txt" 66 circos_file="$outputDir/${sample}_VD_circos.txt"
58 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} 67 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
59 #echo -n "labels" > $outputDir/tmp.txt 68 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
60 #cat ${circos_file} >> $outputDir/tmp.txt 69 /home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1
61 #mv $outputDir/tmp.txt ${circos_file} 70 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png
62 #cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/; /home/galaxy/Downloads/circos-master/bin/circos -param karyotype=$outputDir/circos/karyotype.txt -conf $dir/circos/circos.conf 2>&1 71
72 circos_file="$outputDir/${sample}_DJ_circos.txt"
73 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
74 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
75 /home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1
76 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png
77
78 fi
63 done 79 done
64 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile 80 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
65 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile 81 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
66 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile 82 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile
67 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile 83 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
78 echo "<img src='DPlot.png'/>" >> $outputFile 94 echo "<img src='DPlot.png'/>" >> $outputFile
79 fi 95 fi
80 echo "<img src='JPlot.png'/>" >> $outputFile 96 echo "<img src='JPlot.png'/>" >> $outputFile
81 echo "<img src='AAComposition.png'/></div>" >> $outputFile 97 echo "<img src='AAComposition.png'/></div>" >> $outputFile
82 98
99 #Heatmaps
100
83 count=1 101 count=1
84 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile 102 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
85 for sample in $samples; do 103 for sample in $samples; do
86 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile 104 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile
87 if [[ "$useD" == "true" ]] ; then 105 if [[ "$useD" == "true" ]] ; then
90 echo "<td><img src='HeatmapVJ_$sample.png'/></td>" >> $outputFile 108 echo "<td><img src='HeatmapVJ_$sample.png'/></td>" >> $outputFile
91 if [[ "$useD" == "true" ]] ; then 109 if [[ "$useD" == "true" ]] ; then
92 echo "<td><img src='HeatmapDJ_$sample.png'/></td>" >> $outputFile 110 echo "<td><img src='HeatmapDJ_$sample.png'/></td>" >> $outputFile
93 fi 111 fi
94 echo "</tr></table></div>" >> $outputFile 112 echo "</tr></table></div>" >> $outputFile
113 count=$((count+1))
114 done
115 echo "</div></div>" >> $outputFile
116
117 #circos
118
119 echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile
120 for sample in $samples; do
121 echo "<div class='tabbertab' title='$sample'><table border='1'><center>" >> $outputFile
122 if [[ "$useD" == "true" ]] ; then
123 echo "<tr><td>V-D</td><td><img src='circosVD_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
124 fi
125 echo "<tr><td>V-J</td><td><img src='circosVJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
126 if [[ "$useD" == "true" ]] ; then
127 echo "<tr><td>D-J</td><td><img src='circosDJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
128 fi
129 echo "<center></table></div>" >> $outputFile
95 count=$((count+1)) 130 count=$((count+1))
96 done 131 done
97 echo "</div></div>" >> $outputFile 132 echo "</div></div>" >> $outputFile
98 133
99 #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile 134 #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile