Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 99:86206431cbb0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Thu, 16 Jun 2016 10:01:54 -0400
parents 5ffbf40cdd4b
children ff5be711382b
comparison
equal deleted inserted replaced
98:5ffbf40cdd4b 99:86206431cbb0
91 cat `find $PWD/files/ -name "7_*"` > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt" 91 cat `find $PWD/files/ -name "7_*"` > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
92 cat `find $PWD/files/ -name "8_*"` > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt" 92 cat `find $PWD/files/ -name "8_*"` > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
93 cat `find $PWD/files/ -name "9_*"` > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt" 93 cat `find $PWD/files/ -name "9_*"` > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
94 cat `find $PWD/files/ -name "10_*"` > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt" 94 cat `find $PWD/files/ -name "10_*"` > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
95 95
96 Rscript $dir/tmp/igat.r $outdir/new_IMGT/ $outdir/merged.txt 2>&1 96 mkdir $outdir/new_IMGT_ca
97 cp $outdir/new_IMGT/* $outdir/new_IMGT_ca
98
99 mkdir $outdir/new_IMGT_cg
100 cp $outdir/new_IMGT/* $outdir/new_IMGT_cg
101
102 mkdir $outdir/new_IMGT_cm
103 cp $outdir/new_IMGT/* $outdir/new_IMGT_cm
104
105 Rscript $dir/tmp/igat.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
106 Rscript $dir/tmp/igat.r $outdir/new_IMGT_ca/ $outdir/merged.txt "ca "2>&1
107 Rscript $dir/tmp/igat.r $outdir/new_IMGT_cg/ $outdir/merged.txt "cg "2>&1
108 Rscript $dir/tmp/igat.r $outdir/new_IMGT_cm/ $outdir/merged.txt "cm "2>&1
97 109
98 110
99 tmp="$PWD" 111 tmp="$PWD"
100 cd $outdir/new_IMGT/ #tar weirdness... 112 cd $outdir/new_IMGT/ #tar weirdness...
101 tar -cJf ../new_IMGT.txz * 113 tar -cJf ../new_IMGT.txz *
102
103 cp $dir/tmp/IgAT.xlsm $outdir/new_IMGT/IgAT.xlsm 114 cp $dir/tmp/IgAT.xlsm $outdir/new_IMGT/IgAT.xlsm
104
105 #tar -cJf ../IgAT.txz *
106 zip -r ../IgAT.zip * 115 zip -r ../IgAT.zip *
107 116
117 cd $outdir/new_IMGT_ca/
118 tar -cJf ../new_IMGT_ca.txz *
119 cp $dir/tmp/IgAT.xlsm $outdir/new_IMGT_ca/IgAT.xlsm
120 zip -r ../IgAT_ca.zip *
121
122 cd $outdir/new_IMGT_cg/
123 tar -cJf ../new_IMGT_cg.txz *
124 cp $dir/tmp/IgAT.xlsm $outdir/new_IMGT_cg/IgAT.xlsm
125 zip -r ../IgAT_cg.zip *
126
127 cd $outdir/new_IMGT_cm/
128 tar -cJf ../new_IMGT_cm.txz *
129 cp $dir/tmp/IgAT.xlsm $outdir/new_IMGT_cm/IgAT.xlsm
130 zip -r ../IgAT_cm.zip *
131
108 cd $tmp 132 cd $tmp
109
110 133
111 echo "---------------- mutation_analysis.r ----------------" 134 echo "---------------- mutation_analysis.r ----------------"
112 echo "---------------- mutation_analysis.r ----------------<br />" >> $output 135 echo "---------------- mutation_analysis.r ----------------<br />" >> $output
113 136
114 classes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm,unmatched" 137 classes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm,unmatched"
134 echo "---------------- sequence_overview.r ----------------" >> $output 157 echo "---------------- sequence_overview.r ----------------" >> $output
135 158
136 mkdir $outdir/sequence_overview 159 mkdir $outdir/sequence_overview
137 160
138 #Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1 161 #Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
139 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1 162 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
140 163
141 echo "<table border='1'>" > $outdir/base_overview.html 164 echo "<table border='1'>" > $outdir/base_overview.html
142 165
143 while IFS=$'\t' read ID class seq A C G T 166 while IFS=$'\t' read ID class seq A C G T
144 do 167 do
205 echo "<a href='absent_aa_id.txt'>Absant AA locations by id</a><br />" >> $output 228 echo "<a href='absent_aa_id.txt'>Absant AA locations by id</a><br />" >> $output
206 echo "<a href='sequence_overview/index.html'>Sequence Overview</a><br />" >> $output 229 echo "<a href='sequence_overview/index.html'>Sequence Overview</a><br />" >> $output
207 echo "<a href='base_overview.html'>Base overview</a><br />" >> $output 230 echo "<a href='base_overview.html'>Base overview</a><br />" >> $output
208 echo "<a href='baseline.pdf'>Baseline PDF</a><br />" >> $output 231 echo "<a href='baseline.pdf'>Baseline PDF</a><br />" >> $output
209 echo "<a href='baseline.txt'>Baseline Table</a><br />" >> $output 232 echo "<a href='baseline.txt'>Baseline Table</a><br />" >> $output
233 echo "<a href='baseline_ca.pdf'>Baseline ca PDF</a><br />" >> $output
234 echo "<a href='baseline_ca.txt'>Baseline ca Table</a><br />" >> $output
235 echo "<a href='baseline_cg.pdf'>Baseline cg PDF</a><br />" >> $output
236 echo "<a href='baseline_cg.txt'>Baseline cg Table</a><br />" >> $output
237 echo "<a href='baseline_cm.pdf'>Baseline cm PDF</a><br />" >> $output
238 echo "<a href='baseline_cm.txt'>Baseline cm Table</a><br />" >> $output
210 echo "<a href='IgAT.zip'>IgAT zip</a><br />" >> $output 239 echo "<a href='IgAT.zip'>IgAT zip</a><br />" >> $output
240 echo "<a href='IgAT_ca.zip'>IgAT ca zip</a><br />" >> $output
241 echo "<a href='IgAT_cg.zip'>IgAT cg zip</a><br />" >> $output
242 echo "<a href='IgAT_cm.zip'>IgAT cm zip</a><br />" >> $output
243 echo "<a href='new_IMGT.txz'>Filtered IMGT zip</a><br />" >> $output
244 echo "<a href='new_IMGT_ca.txz'>Filtered ca IMGT zip</a><br />" >> $output
245 echo "<a href='new_IMGT_cg.txz'>Filtered cg IMGT zip</a><br />" >> $output
246 echo "<a href='new_IMGT_cm.txz'>Filtered cm IMGT zip</a><br />" >> $output
247
211 248
212 echo "---------------- images ----------------" 249 echo "---------------- images ----------------"
213 250
214 echo "<img src='all.png'/><br />" >> $output 251 echo "<img src='all.png'/><br />" >> $output
215 echo "<a href='all.txt'>download data</a><br />" >> $output 252 echo "<a href='all.txt'>download data</a><br />" >> $output
258 echo "</table>" >> $output 295 echo "</table>" >> $output
259 296
260 echo "</html>" >> $output 297 echo "</html>" >> $output
261 298
262 echo "---------------- baseline ----------------" 299 echo "---------------- baseline ----------------"
263 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "sample name" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt" 300 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "ca_cg_cm" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
301 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_ca.txz "ca" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_ca.pdf" "Sequence.ID" "$outdir/baseline_ca.txt"
302 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cg.txz "cg" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cg.pdf" "Sequence.ID" "$outdir/baseline_cg.txt"
303 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cm.txz "cm" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cm.pdf" "Sequence.ID" "$outdir/baseline_cm.txt"
264 304
265 #optional output for naive 305 #optional output for naive
266 306
267 echo "---------------- naive_output.r ----------------" 307 echo "---------------- naive_output.r ----------------"
268 308
278 318
279 echo "</table>" >> $outdir/base_overview.html 319 echo "</table>" >> $outdir/base_overview.html
280 320
281 echo "---------------- Done! ----------------" 321 echo "---------------- Done! ----------------"
282 322
283
284
285
286
287
288
289 #rm $outdir/HS12RSS.txt
290 #rm $outdir/HS23RSS.txt