Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 17:ee1bda8c27c8 draft

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author davidvanzessen
date Mon, 09 Nov 2015 08:28:31 -0500
parents f90fbc15b35a
children f2010de70741
comparison
equal deleted inserted replaced
16:cf1def1aaa74 17:ee1bda8c27c8
135 fi 135 fi
136 done 136 done
137 echo "</div></div>" >> $outputFile 137 echo "</div></div>" >> $outputFile
138 fi 138 fi
139 139
140 hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)" 140 hasJunctionData="$(if head -n 1 $inputFile | grep -qE '3V.REGION.trimmed.nt.nb'; then echo 'Yes'; else echo 'No'; fi)"
141 141
142 if [[ "$hasJunctionData" == "Yes" ]] ; then 142 if [[ "$hasJunctionData" == "Yes" ]] ; then
143 echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile 143 echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile
144 echo "<table border='1' id='junction_table'> <caption>Productive</caption><thead><tr><th>Sample</th><th>count</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile 144 echo "<table border='1' id='junction_table'> <caption>Productive</caption><thead><tr><th>Sample</th><th>count</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile
145 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP 145 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP