Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 1:856b5b718d21 draft

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author davidvanzessen
date Mon, 18 Aug 2014 04:42:59 -0400
parents 74d2bc479bee
children 2f4298673519
comparison
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0:74d2bc479bee 1:856b5b718d21
2 dir="$(cd "$(dirname "$0")" && pwd)" 2 dir="$(cd "$(dirname "$0")" && pwd)"
3 3
4 input=$1 4 input=$1
5 output=$2 5 output=$2
6 outdir=$3 6 outdir=$3
7 title=$4
7 mkdir $outdir 8 mkdir $outdir
8 9
9 unzip $input -d $PWD/files/ > $PWD/unziplog.log 10 unzip $input -d $PWD/files/ > $PWD/unziplog.log
10 cat $PWD/files/*/1_* > $PWD/summary.txt 11 cat $PWD/files/*/1_* > $PWD/summary.txt
11 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt 12 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
72 cm_n=`cat $outdir/cm/n.txt` 73 cm_n=`cat $outdir/cm/n.txt`
73 #all_n=$((ca_n + cg_n + cm_n)) 74 #all_n=$((ca_n + cg_n + cm_n))
74 all_n=`cat $outdir/n.txt` 75 all_n=`cat $outdir/n.txt`
75 76
76 77
77 echo "<html><table border='1'>" > $output 78 echo "<html><center><h1>$title</h1></center><table border='1'>" > $output
78 echo "<tr><th>info</th>" >> $output 79 echo "<tr><th>info</th>" >> $output
79 echo "<th><a href='identification/ca.txt'>ca (N = $ca_n)</a></th>" >> $output 80 echo "<th><a href='identification/ca.txt'>ca (N = $ca_n)</a></th>" >> $output
80 echo "<th><a href='identification/ca1.txt'>ca1 (N = $ca1_n)</a></th>" >> $output 81 echo "<th><a href='identification/ca1.txt'>ca1 (N = $ca1_n)</a></th>" >> $output
81 echo "<th><a href='identification/ca2.txt'>ca2 (N = $ca2_n)</a></th>" >> $output 82 echo "<th><a href='identification/ca2.txt'>ca2 (N = $ca2_n)</a></th>" >> $output
82 echo "<th><a href='identification/cg.txt'>cg (N = $cg_n)</a></th>" >> $output 83 echo "<th><a href='identification/cg.txt'>cg (N = $cg_n)</a></th>" >> $output