Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 26:2433a1e110e1 draft

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Uploaded
author davidvanzessen
date Wed, 08 Apr 2015 05:25:52 -0400
parents 58a62d2c0377
children c623690e3b81
comparison
equal deleted inserted replaced
25:58a62d2c0377 26:2433a1e110e1
13 cat $PWD/files/*/1_* > $PWD/summary.txt 13 cat $PWD/files/*/1_* > $PWD/summary.txt
14 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt 14 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
15 cat $PWD/files/*/8_* > $PWD/mutationstats.txt 15 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
16 cat $PWD/files/*/10_* > $PWD/hotspots.txt 16 cat $PWD/files/*/10_* > $PWD/hotspots.txt
17 17
18 BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin" 18 #BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin"
19 19
20 echo "${BLASTN_DIR}" 20 echo "${BLASTN_DIR}"
21
22
23
24 21
25 echo "identification ($method)" 22 echo "identification ($method)"
26 23
27 if [[ "${method}" == "custom" ]] ; then 24 if [[ "${method}" == "custom" ]] ; then
28 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt 25 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
48 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm" 45 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
49 echo "R mutation analysis" 46 echo "R mutation analysis"
50 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1 47 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1
51 echo "python mutation analysis" 48 echo "python mutation analysis"
52 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --output $outdir/hotspot_analysis.txt 49 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --output $outdir/hotspot_analysis.txt
50 echo "R AA histogram"
51 Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png 2>&1
53 52
54 cat $outdir/mutations.txt $outdir/hotspot_analysis.txt > $outdir/result.txt 53 cat $outdir/mutations.txt $outdir/hotspot_analysis.txt > $outdir/result.txt
55 54
56 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm) 55 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm)
57 56
77 echo "</table>" >> $output 76 echo "</table>" >> $output
78 echo "<a href='unmatched.txt'>unmatched</a><br /><a href='motif_per_seq.txt'>motif per sequence</a><br />" >> $output 77 echo "<a href='unmatched.txt'>unmatched</a><br /><a href='motif_per_seq.txt'>motif per sequence</a><br />" >> $output
79 78
80 79
81 echo "<img src='all.png'/><br />" >> $output 80 echo "<img src='all.png'/><br />" >> $output
81 echo "<a href='all.txt'>download data</a><br />" >> $output
82 if [ -a $outdir/ca.png ] 82 if [ -a $outdir/ca.png ]
83 then 83 then
84 echo "<img src='ca.png'/><br />" >> $output 84 echo "<img src='ca.png'/><br />" >> $output
85 echo "<a href='ca.txt'>download data</a><br />" >> $output
85 fi 86 fi
86 if [ -a $outdir/cg.png ] 87 if [ -a $outdir/cg.png ]
87 then 88 then
88 echo "<img src='cg.png'/><br />" >> $output 89 echo "<img src='cg.png'/><br />" >> $output
90 echo "<a href='cg.txt'>download data</a><br />" >> $output
89 fi 91 fi
90 if [ -a $outdir/scatter.png ] 92 if [ -a $outdir/scatter.png ]
91 then 93 then
92 echo "<img src='scatter.png'/><br />" >> $output 94 echo "<img src='scatter.png'/><br />" >> $output
95 echo "<a href='scatter.txt'>download data</a><br />" >> $output
96 fi
97 if [ -a $outdir/aa_histogram.png ]
98 then
99 echo "<img src='aa_histogram.png'/><br />" >> $output
100 echo "<a href='aa_histogram.txt'>download data</a><br />" >> $output
93 fi 101 fi
94 102
95 for gene in ${genes[@]} 103 for gene in ${genes[@]}
96 do 104 do
97 echo "<table border='1'><caption>$gene transition table</caption>" >> $output 105 echo "<table border='1'><caption>$gene transition table</caption>" >> $output