Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 78:b523ce95d857 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Wed, 11 May 2016 10:29:33 -0400
parents c5c86d15cb94
children 0513b46178c4
comparison
equal deleted inserted replaced
77:c5c86d15cb94 78:b523ce95d857
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" 89 genes="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 $genes $outdir ${include_fr1} 2>&1
92 92
93 #echo "." > $output 93 #echo "." > $output
94 #exit 0 94 #exit 0
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 $genes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt
102 echo "R AA histogram"
103 102
104 echo "---------------- aa_histogram.r ----------------" 103 echo "---------------- aa_histogram.r ----------------"
105 echo "---------------- aa_histogram.r ----------------<br />" >> $output 104 echo "---------------- aa_histogram.r ----------------<br />" >> $output
106 105
107 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
139 for gene in ${genes[@]} 138 for gene in ${genes[@]}
140 do 139 do
141 tmp=`cat $outdir/${gene}_${func}_n.txt` 140 tmp=`cat $outdir/${gene}_${func}_n.txt`
142 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output 141 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
143 done 142 done
143
144 tmp=`cat $outdir/unmatched_${func}_n.txt`
145 echo "<th><a href='unmatched.txt'>unmatched (N = $tmp)</a></th>" >> $output
144 tmp=`cat $outdir/all_${func}_n.txt` 146 tmp=`cat $outdir/all_${func}_n.txt`
145 echo "<th><a href='matched_all.txt'>all (N = $tmp)</a></th>" >> $output 147 echo "<th><a href='matched_${func}_all.txt'>all (N = $tmp)</a></th>" >> $output
146 148
147 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz allx ally allz 149 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz unx uny unz allx ally allz
148 do 150 do
149 if [ "$name" == "FR S/R (ratio)" ] || [ "$name" == "CDR S/R (ratio)" ] ; then #meh 151 if [ "$name" == "FR S/R (ratio)" ] || [ "$name" == "CDR S/R (ratio)" ] ; then #meh
150 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz})</td><td>${ca1x}/${ca1y} (${ca1z})</td><td>${ca2x}/${ca2y} (${ca2z})</td><td>${cgx}/${cgy} (${cgz})</td><td>${cg1x}/${cg1y} (${cg1z})</td><td>${cg2x}/${cg2y} (${cg2z})</td><td>${cg3x}/${cg3y} (${cg3z})</td><td>${cg4x}/${cg4y} (${cg4z})</td><td>${cmx}/${cmy} (${cmz})</td><td>${allx}/${ally} (${allz})</td></tr>" >> $output 152 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz})</td><td>${ca1x}/${ca1y} (${ca1z})</td><td>${ca2x}/${ca2y} (${ca2z})</td><td>${cgx}/${cgy} (${cgz})</td><td>${cg1x}/${cg1y} (${cg1z})</td><td>${cg2x}/${cg2y} (${cg2z})</td><td>${cg3x}/${cg3y} (${cg3z})</td><td>${cg4x}/${cg4y} (${cg4z})</td><td>${cmx}/${cmy} (${cmz})</td><td>${allx}/${ally} (${allz})</td></tr>" >> $output
151 else 153 else
152 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz}%)</td><td>${ca1x}/${ca1y} (${ca1z}%)</td><td>${ca2x}/${ca2y} (${ca2z}%)</td><td>${cgx}/${cgy} (${cgz}%)</td><td>${cg1x}/${cg1y} (${cg1z}%)</td><td>${cg2x}/${cg2y} (${cg2z}%)</td><td>${cg3x}/${cg3y} (${cg3z}%)</td><td>${cg4x}/${cg4y} (${cg4z}%)</td><td>${cmx}/${cmy} (${cmz}%)</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output 154 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz}%)</td><td>${ca1x}/${ca1y} (${ca1z}%)</td><td>${ca2x}/${ca2y} (${ca2z}%)</td><td>${cgx}/${cgy} (${cgz}%)</td><td>${cg1x}/${cg1y} (${cg1z}%)</td><td>${cg2x}/${cg2y} (${cg2z}%)</td><td>${cg3x}/${cg3y} (${cg3z}%)</td><td>${cg4x}/${cg4y} (${cg4z}%)</td><td>${cmx}/${cmy} (${cmz}%)</td><td>${unx}/${uny} (${unz}%)</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
153 fi 155 fi
154 done < $outdir/result.txt 156 done < $outdir/result.txt
155 157
156 done 158 done
157 159