Mercurial > repos > davidvanzessen > report_clonality_igg

comparison r_wrapper.sh @ 27:f919965e8816 draft

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author davidvanzessen
date Fri, 06 Mar 2015 09:59:53 -0500
parents 5454af6fece1
children
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26:01f05258f672 27:f919965e8816
5 outputFile=$3/index.html #$2 5 outputFile=$3/index.html #$2
6 clonalType=$4 6 clonalType=$4
7 species=$5 7 species=$5
8 locus=$6 8 locus=$6
9 filterproductive=$7 9 filterproductive=$7
10 clonality_method=$8
10 dir="$(cd "$(dirname "$0")" && pwd)" 11 dir="$(cd "$(dirname "$0")" && pwd)"
11 useD="false" 12 useD="false"
12 if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then 13 if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then
13 echo "species D region in reference db" 14 echo "species D region in reference db"
14 useD="true" 15 useD="true"
20 echo "${loci[@]}" 21 echo "${loci[@]}"
21 if [[ "${#loci[@]}" -eq "2" ]] ; then 22 if [[ "${#loci[@]}" -eq "2" ]] ; then
22 useD="false" 23 useD="false"
23 fi 24 fi
24 fi 25 fi
26 useD="false"
25 mkdir $3 27 mkdir $3
26 cp $dir/genes.txt $outputDir 28 cp $dir/genes.txt $outputDir
27 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive 2>&1 29 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive ${clonality_method} 2>&1
28 cp $dir/tabber.js $outputDir 30 cp $dir/tabber.js $outputDir
29 cp $dir/style.css $outputDir 31 cp $dir/style.css $outputDir
30 cp $dir/script.js $outputDir 32 cp $dir/script.js $outputDir
31 cp $dir/jquery-1.11.0.min.js $outputDir 33 cp $dir/jquery-1.11.0.min.js $outputDir
32 samples=`cat $outputDir/samples.txt` 34 samples=`cat $outputDir/samples.txt`
87 #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile 89 #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile
88 90
89 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)" 91 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
90 echo "$hasReplicateColumn" 92 echo "$hasReplicateColumn"
91 #if its a 'new' merged file with replicate info 93 #if its a 'new' merged file with replicate info
92 if [[ "$hasReplicateColumn" == "Yes" ]] ; then 94 if [[ "$hasReplicateColumn" == "Yes" && "$clonalType" != "none" ]] ; then
93 echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile 95 echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile
94 for sample in $samples; do 96 for sample in $samples; do
95 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)" 97 echo "${clonality_method}"
96 echo "<div class='tabbertab' title='$sample'><table border='1'>" >> $outputFile 98 if [[ "${clonality_method}" == "old" ]] ; then
97 echo "<tr><td colspan='4'>Clonality Score: $clonalityScore</td></tr>" >> $outputFile 99 echo "in old"
98 100 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
99 #replicate,reads,squared 101 echo "<div class='tabbertab' title='$sample'><table border='1'>" >> $outputFile
100 echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile 102 echo "<tr><td colspan='4'>Clonality Score: $clonalityScore</td></tr>" >> $outputFile
101 while IFS=, read replicate reads squared 103
102 do 104 #replicate,reads,squared
105 echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
106 while IFS=, read replicate reads squared
107 do
108
109 echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile
110 done < $outputDir/ReplicateReads_$sample.csv
103 111
104 echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile 112 #sum of reads and reads squared
105 done < $outputDir/ReplicateReads_$sample.csv 113 while IFS=, read readsSum squaredSum
106 114 do
107 #sum of reads and reads squared 115 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
108 while IFS=, read readsSum squaredSum 116 done < $outputDir/ReplicateSumReads_$sample.csv
117
118 #overview
119 echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile
120 while IFS=, read type count weight weightedCount
109 do 121 do
110 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile 122 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
111 done < $outputDir/ReplicateSumReads_$sample.csv 123 done < $outputDir/ClonalityOverView_$sample.csv
112 124 echo "</table></div>" >> $outputFile
113 #overview 125 else
114 echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile 126 echo "in new"
115 while IFS=, read type count weight weightedCount 127 clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.csv)"
116 do 128 echo "<div class='tabbertab' title='$sample'>" >> $outputFile
117 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile 129 echo "Lymphclon clonality score: <br />$clonalityScore<br /><br />" >> $outputFile
118 done < $outputDir/ClonalityOverView_$sample.csv 130 echo "<table border = 1>" >> $outputFile
119 echo "</table></div>" >> $outputFile 131 while IFS=, read type count
132 do
133 echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile
134 done < $outputDir/lymphclon_coincidences_$sample.csv
135 echo "</table></div>" >> $outputFile
136 fi
120 done 137 done
121 echo "</div></div>" >> $outputFile 138 echo "</div></div>" >> $outputFile
122 fi 139 fi
123 140
124 hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)" 141 hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)"