Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 49:5c6b9e99d576 draft

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author davidvanzessen
date Wed, 18 Nov 2015 05:55:04 -0500
parents 099cc1254f74
children 8ba6afa1247a
comparison
equal deleted inserted replaced
48:d09b1bdfd388 49:5c6b9e99d576
64 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1 64 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1
65 echo "python mutation analysis" 65 echo "python mutation analysis"
66 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt 66 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt
67 echo "R AA histogram" 67 echo "R AA histogram"
68 Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png 2>&1 68 Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png 2>&1
69
70 cat $outdir/mutations.txt $outdir/hotspot_analysis.txt > $outdir/result.txt 69 cat $outdir/mutations.txt $outdir/hotspot_analysis.txt > $outdir/result.txt
71 70
72 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm) 71 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm)
73 72
74 73
89 else 88 else
90 echo "<tr><td>$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>" >> $output 89 echo "<tr><td>$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
91 fi 90 fi
92 done < $outdir/result.txt 91 done < $outdir/result.txt
93 echo "</table>" >> $output 92 echo "</table>" >> $output
94 echo "<a href='unmatched.txt'>unmatched</a><br /><a href='motif_per_seq.txt'>motif per sequence</a><br /><a href='merged.txt'>all data</a><br /><a href='mutation_by_id.txt'>mutations by id</a><br /><a href='aa_id_mutations.txt'>AA mutations location by id</a><br />" >> $output 93 echo "<a href='unmatched.txt'>unmatched</a><br /><a href='motif_per_seq.txt'>motif per sequence</a><br /><a href='merged.txt'>all data</a><br /><a href='mutation_by_id.txt'>mutations by id</a><br /><a href='aa_id_mutations.txt'>AA mutations location by id</a><br /><a href='absent_aa_id.txt'>Absant AA locations by id</a><br />" >> $output
95 94
96 95
97 echo "<img src='all.png'/><br />" >> $output 96 echo "<img src='all.png'/><br />" >> $output
98 echo "<a href='all.txt'>download data</a><br />" >> $output 97 echo "<a href='all.txt'>download data</a><br />" >> $output
99 if [ -a $outdir/ca.png ] 98 if [ -a $outdir/ca.png ]
108 fi 107 fi
109 if [ -a $outdir/scatter.png ] 108 if [ -a $outdir/scatter.png ]
110 then 109 then
111 echo "<img src='scatter.png'/><br />" >> $output 110 echo "<img src='scatter.png'/><br />" >> $output
112 echo "<a href='scatter.txt'>download data</a><br />" >> $output 111 echo "<a href='scatter.txt'>download data</a><br />" >> $output
112 fi
113 if [ -a $outdir/frequency_ranges.png ]
114 then
115 echo "<img src='frequency_ranges.png'/><br />" >> $output
116 echo "<a href='frequency_ranges_classes.txt'>download class data</a><br />" >> $output
117 echo "<a href='frequency_ranges_subclasses.txt'>download subclass data</a><br />" >> $output
113 fi 118 fi
114 if [ -a $outdir/aa_histogram.png ] 119 if [ -a $outdir/aa_histogram.png ]
115 then 120 then
116 echo "<img src='aa_histogram.png'/><br />" >> $output 121 echo "<img src='aa_histogram.png'/><br />" >> $output
117 echo "<a href='aa_histogram.txt'>download data</a><br />" >> $output 122 echo "<a href='aa_histogram.txt'>download data</a><br />" >> $output