Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 22:d84c9791d8c4 draft

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Uploaded
author davidvanzessen
date Tue, 07 Apr 2015 03:52:34 -0400
parents c9f9623f1f76
children 58a62d2c0377
comparison
equal deleted inserted replaced
21:c9f9623f1f76 22:d84c9791d8c4
4 input=$1 4 input=$1
5 method=$2 5 method=$2
6 output=$3 6 output=$3
7 outdir=$4 7 outdir=$4
8 title=$5 8 title=$5
9 include_fr1=$6
9 mkdir $outdir 10 mkdir $outdir
10 11
11 unzip $input -d $PWD/files/ > $PWD/unziplog.log 12 unzip $input -d $PWD/files/ > $PWD/unziplog.log
12 cat $PWD/files/*/1_* > $PWD/summary.txt 13 cat $PWD/files/*/1_* > $PWD/summary.txt
13 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt 14 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
14 cat $PWD/files/*/8_* > $PWD/mutationstats.txt 15 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
15 cat $PWD/files/*/10_* > $PWD/hotspots.txt 16 cat $PWD/files/*/10_* > $PWD/hotspots.txt
16 17
17 #BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin" 18 BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin"
18 19
19 echo "${BLASTN_DIR}" 20 echo "${BLASTN_DIR}"
20 21
21 22
22 23
44 echo "merging" 45 echo "merging"
45 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method 46 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method
46 47
47 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm" 48 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
48 echo "R mutation analysis" 49 echo "R mutation analysis"
49 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir 2>&1 50 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1
50 echo "python mutation analysis" 51 echo "python mutation analysis"
51 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --output $outdir/hotspot_analysis.txt 52 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --output $outdir/hotspot_analysis.txt
52 53
53 cat $outdir/mutations.txt $outdir/hotspot_analysis.txt > $outdir/result.txt 54 cat $outdir/mutations.txt $outdir/hotspot_analysis.txt > $outdir/result.txt
54 55
80 fi 81 fi
81 if [ -a $outdir/cg.png ] 82 if [ -a $outdir/cg.png ]
82 then 83 then
83 echo "<img src='cg.png'/><br />" >> $output 84 echo "<img src='cg.png'/><br />" >> $output
84 fi 85 fi
86 if [ -a $outdir/scatter.png ]
87 then
88 echo "<img src='scatter.png'/><br />" >> $output
89 fi
85 90
86 for gene in ${genes[@]} 91 for gene in ${genes[@]}
87 do 92 do
88 echo "<table border='1'><caption>$gene transition table</caption>" >> $output 93 echo "<table border='1'><caption>$gene transition table</caption>" >> $output
89 while IFS=, read from a c g t 94 while IFS=, read from a c g t