Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 116:4984c2a06c43 draft

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Uploaded
author davidvanzessen
date Wed, 10 Aug 2016 08:20:17 -0400
parents e7b550d52eb7
children a8f91c52411c
comparison
equal deleted inserted replaced
115:ede6c4ee5196 116:4984c2a06c43
100 cat `find $PWD/files/ -name "10_*"` > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt" 100 cat `find $PWD/files/ -name "10_*"` > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
101 101
102 mkdir $outdir/new_IMGT_ca 102 mkdir $outdir/new_IMGT_ca
103 cp $outdir/new_IMGT/* $outdir/new_IMGT_ca 103 cp $outdir/new_IMGT/* $outdir/new_IMGT_ca
104 104
105 mkdir $outdir/new_IMGT_ca1
106 cp $outdir/new_IMGT/* $outdir/new_IMGT_ca1
107
108 mkdir $outdir/new_IMGT_ca2
109 cp $outdir/new_IMGT/* $outdir/new_IMGT_ca2
110
105 mkdir $outdir/new_IMGT_cg 111 mkdir $outdir/new_IMGT_cg
106 cp $outdir/new_IMGT/* $outdir/new_IMGT_cg 112 cp $outdir/new_IMGT/* $outdir/new_IMGT_cg
107 113
114 mkdir $outdir/new_IMGT_cg1
115 cp $outdir/new_IMGT/* $outdir/new_IMGT_cg1
116
117 mkdir $outdir/new_IMGT_cg2
118 cp $outdir/new_IMGT/* $outdir/new_IMGT_cg2
119
120 mkdir $outdir/new_IMGT_cg3
121 cp $outdir/new_IMGT/* $outdir/new_IMGT_cg3
122
123 mkdir $outdir/new_IMGT_cg4
124 cp $outdir/new_IMGT/* $outdir/new_IMGT_cg4
125
108 mkdir $outdir/new_IMGT_cm 126 mkdir $outdir/new_IMGT_cm
109 cp $outdir/new_IMGT/* $outdir/new_IMGT_cm 127 cp $outdir/new_IMGT/* $outdir/new_IMGT_cm
110 128
111 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1 129 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
130
112 Rscript $dir/new_imgt.r $outdir/new_IMGT_ca/ $outdir/merged.txt "ca" 2>&1 131 Rscript $dir/new_imgt.r $outdir/new_IMGT_ca/ $outdir/merged.txt "ca" 2>&1
132 Rscript $dir/new_imgt.r $outdir/new_IMGT_ca1/ $outdir/merged.txt "ca1" 2>&1
133 Rscript $dir/new_imgt.r $outdir/new_IMGT_ca2/ $outdir/merged.txt "ca2" 2>&1
134
113 Rscript $dir/new_imgt.r $outdir/new_IMGT_cg/ $outdir/merged.txt "cg" 2>&1 135 Rscript $dir/new_imgt.r $outdir/new_IMGT_cg/ $outdir/merged.txt "cg" 2>&1
136 Rscript $dir/new_imgt.r $outdir/new_IMGT_cg1/ $outdir/merged.txt "cg1" 2>&1
137 Rscript $dir/new_imgt.r $outdir/new_IMGT_cg2/ $outdir/merged.txt "cg2" 2>&1
138 Rscript $dir/new_imgt.r $outdir/new_IMGT_cg3/ $outdir/merged.txt "cg3" 2>&1
139 Rscript $dir/new_imgt.r $outdir/new_IMGT_cg4/ $outdir/merged.txt "cg4" 2>&1
140
114 Rscript $dir/new_imgt.r $outdir/new_IMGT_cm/ $outdir/merged.txt "cm" 2>&1 141 Rscript $dir/new_imgt.r $outdir/new_IMGT_cm/ $outdir/merged.txt "cm" 2>&1
115 142
116 143
117 tmp="$PWD" 144 tmp="$PWD"
118 cd $outdir/new_IMGT/ #tar weirdness... 145 cd $outdir/new_IMGT/ #tar weirdness...
345 #echo "<tr><td></td><td><a href='IgAT_ca.zip'>IgAT ca zip</a></td></tr>" >> $output 372 #echo "<tr><td></td><td><a href='IgAT_ca.zip'>IgAT ca zip</a></td></tr>" >> $output
346 #echo "<tr><td></td><td><a href='IgAT_cg.zip'>IgAT cg zip</a></td></tr>" >> $output 373 #echo "<tr><td></td><td><a href='IgAT_cg.zip'>IgAT cg zip</a></td></tr>" >> $output
347 #echo "<tr><td></td><td><a href='IgAT_cm.zip'>IgAT cm zip</a></td></tr>" >> $output 374 #echo "<tr><td></td><td><a href='IgAT_cm.zip'>IgAT cm zip</a></td></tr>" >> $output
348 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz'>Download</a></td></tr>" >> $output 375 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz'>Download</a></td></tr>" >> $output
349 echo "<tr><td>An IMGT archive with just the matched and filtered ca sequences</td><td><a href='new_IMGT_ca.txz'>Download</a></td></tr>" >> $output 376 echo "<tr><td>An IMGT archive with just the matched and filtered ca sequences</td><td><a href='new_IMGT_ca.txz'>Download</a></td></tr>" >> $output
377 echo "<tr><td>An IMGT archive with just the matched and filtered ca1 sequences</td><td><a href='new_IMGT_ca1.txz'>Download</a></td></tr>" >> $output
378 echo "<tr><td>An IMGT archive with just the matched and filtered ca2 sequences</td><td><a href='new_IMGT_ca2.txz'>Download</a></td></tr>" >> $output
350 echo "<tr><td>An IMGT archive with just the matched and filtered cg sequences</td><td><a href='new_IMGT_cg.txz'>Download</a></td></tr>" >> $output 379 echo "<tr><td>An IMGT archive with just the matched and filtered cg sequences</td><td><a href='new_IMGT_cg.txz'>Download</a></td></tr>" >> $output
380 echo "<tr><td>An IMGT archive with just the matched and filtered cg1 sequences</td><td><a href='new_IMGT_cg1.txz'>Download</a></td></tr>" >> $output
381 echo "<tr><td>An IMGT archive with just the matched and filtered cg2 sequences</td><td><a href='new_IMGT_cg2.txz'>Download</a></td></tr>" >> $output
382 echo "<tr><td>An IMGT archive with just the matched and filtered cg3 sequences</td><td><a href='new_IMGT_cg3.txz'>Download</a></td></tr>" >> $output
383 echo "<tr><td>An IMGT archive with just the matched and filtered cg4 sequences</td><td><a href='new_IMGT_cg4.txz'>Download</a></td></tr>" >> $output
351 echo "<tr><td>An IMGT archive with just the matched and filtered cm sequences</td><td><a href='new_IMGT_cm.txz'>Download</a></td></tr>" >> $output 384 echo "<tr><td>An IMGT archive with just the matched and filtered cm sequences</td><td><a href='new_IMGT_cm.txz'>Download</a></td></tr>" >> $output
352 echo "</table>" >> $output 385 echo "</table>" >> $output
353 386
354 echo "</div>" >> $output #downloads tab end 387 echo "</div>" >> $output #downloads tab end
355 388