Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 64:55f18bf19d72 draft

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author davidvanzessen
date Fri, 29 Apr 2016 09:08:45 -0400
parents a073fa12ef98
children 69a6bba9ada9
comparison
equal deleted inserted replaced
63:bd6fb6c03948 64:55f18bf19d72
162 162
163 #replicate,reads,squared 163 #replicate,reads,squared
164 echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile 164 echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
165 while IFS=, read replicate reads squared 165 while IFS=, read replicate reads squared
166 do 166 do
167
168 echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile 167 echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile
169 done < $outputDir/ReplicateReads_$sample.csv 168 done < $outputDir/ReplicateReads_$sample.csv
170 169
171 #sum of reads and reads squared 170 #sum of reads and reads squared
172 while IFS=, read readsSum squaredSum 171 while IFS=, read readsSum squaredSum
176 175
177 #overview 176 #overview
178 echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile 177 echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile
179 while IFS=, read type count weight weightedCount 178 while IFS=, read type count weight weightedCount
180 do 179 do
181 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile 180 if [[ "$type" -eq "1" ]]; then
181 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
182 else
183 echo "<tr><td><a href='coincidences_${sample}_${type}.txt'>$type</a></td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
184 fi
185
182 done < $outputDir/ClonalityOverView_$sample.csv 186 done < $outputDir/ClonalityOverView_$sample.csv
183 echo "</table></div>" >> $outputFile 187 echo "</table></div>" >> $outputFile
184 else 188 else
185 echo "in new" 189 echo "in new"
186 clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.csv)" 190 clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.csv)"