Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 82:564c4f6da203 draft

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author davidvanzessen
date Tue, 24 May 2016 03:52:14 -0400
parents a778156dad3d
children 041f94f50b34
comparison
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81:a778156dad3d 82:564c4f6da203
84 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} 84 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter}
85 85
86 echo "---------------- mutation_analysis.r ----------------" 86 echo "---------------- mutation_analysis.r ----------------"
87 echo "---------------- mutation_analysis.r ----------------<br />" >> $output 87 echo "---------------- mutation_analysis.r ----------------<br />" >> $output
88 88
89 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm,unmatched" 89 classes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm,unmatched"
90 echo "R mutation analysis" 90 echo "R mutation analysis"
91 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1 91 Rscript $dir/mutation_analysis.r $outdir/merged.txt $classes $outdir ${include_fr1} 2>&1
92 92
93 #echo "." > $output 93 #echo "." > $output
94 #exit 0 94 #exit 0
95 95
96 96
97 97
98 echo "---------------- mutation_analysis.py ----------------" 98 echo "---------------- mutation_analysis.py ----------------"
99 echo "---------------- mutation_analysis.py ----------------<br />" >> $output 99 echo "---------------- mutation_analysis.py ----------------<br />" >> $output
100 100
101 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt 101 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $classes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt
102 102
103 echo "---------------- aa_histogram.r ----------------" 103 echo "---------------- aa_histogram.r ----------------"
104 echo "---------------- aa_histogram.r ----------------<br />" >> $output 104 echo "---------------- aa_histogram.r ----------------<br />" >> $output
105 105
106 Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png 2>&1 106 Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png 2>&1
107 107
108 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm) 108 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm)
109 109
110 funcs=(sum mean median) 110 funcs=(sum mean median)
111
112 echo "---------------- sequence_overview.r ----------------"
113
114 mkdir $outdir/sequence_overview
115
116 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
117
118 echo "<table border='1'>" > $outdir/base_overview.html
119
120 while read ID class seq A C G T
121 do
122 echo "<tr><td>$ID</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html
123 done < $outdir/sequence_overview/ntoverview.txt
111 124
112 125
113 echo "<html><center><h1>$title</h1></center>" > $output 126 echo "<html><center><h1>$title</h1></center>" > $output
114 127
115 #display the matched/unmatched for clearity 128 #display the matched/unmatched for clearity
220 echo "</html>" >> $output 233 echo "</html>" >> $output
221 234
222 235
223 #optional output for naive 236 #optional output for naive
224 237
225 echo "---------------- aa_histogram.r ----------------" 238 echo "---------------- naive_output.r ----------------"
226 239
227 if [[ "$naive_output" != "None" ]] 240 if [[ "$naive_output" != "None" ]]
228 then 241 then
229 echo "---------------- imgt_loader.r ----------------" 242 echo "---------------- imgt_loader.r ----------------"
230 #python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output 243 #python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output
231 Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt $outdir/loader_output.txt 2>&1 244 Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt $outdir/loader_output.txt 2>&1
232 echo "---------------- naive_output.r ----------------" 245 echo "---------------- naive_output.r ----------------"
233 Rscript $dir/naive_output.r $outdir/loader_output.txt $outdir/merged.txt ${naive_output_ca} ${naive_output_cg} ${naive_output_cm} $outdir/ntoverview.txt $outdir/ntsum.txt 2>&1 246 Rscript $dir/naive_output.r $outdir/loader_output.txt $outdir/merged.txt ${naive_output_ca} ${naive_output_cg} ${naive_output_cm} $outdir/ntoverview.txt $outdir/ntsum.txt 2>&1
234 fi 247 fi
235 248
236 echo "---------------- sequence_overview.r ----------------"
237
238 mkdir $outdir/sequence_overview
239
240 Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/sequence_overview 2>&1
241
242 echo "<table border='1'>" > $outdir/base_overview.html
243
244 while read ID class seq A C G T
245 do
246 echo "<tr><td>$ID</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html
247 done < $outdir/sequence_overview/ntoverview.txt
248
249 echo "</table>" >> $outdir/base_overview.html 249 echo "</table>" >> $outdir/base_overview.html
250 250
251 echo "---------------- Done! ----------------" 251 echo "---------------- Done! ----------------"
252 252
253 253