Mercurial > repos > davidvanzessen > mutation_analysis
diff wrapper.sh @ 0:74d2bc479bee draft
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| author | davidvanzessen |
|---|---|
| date | Mon, 18 Aug 2014 04:04:37 -0400 |
| parents | |
| children | 856b5b718d21 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/wrapper.sh Mon Aug 18 04:04:37 2014 -0400 @@ -0,0 +1,121 @@ +#!/bin/bash +dir="$(cd "$(dirname "$0")" && pwd)" + +input=$1 +output=$2 +outdir=$3 +mkdir $outdir + +unzip $input -d $PWD/files/ > $PWD/unziplog.log +cat $PWD/files/*/1_* > $PWD/summary.txt +cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt +cat $PWD/files/*/8_* > $PWD/mutationstats.txt +cat $PWD/files/*/10_* > $PWD/hotspots.txt + +mkdir $outdir/identification/ +python $dir/gene_identification.py --input $PWD/summary.txt --outdir $outdir/identification/ +genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm) +tmp=$PWD/tmp +tmp2=$PWD/tmp2 +hotspottmp=$PWD/hotspottmp +mutationtmp=$PWD/mutationtmp +touch $outdir/mutationandhotspot.txt +for gene in ${genes[@]} +do + echo "Running $gene <br />" >> $output + mkdir $outdir/$gene + echo "Filtering input..." >> $output + Rscript $dir/filter.r $PWD/summary.txt $outdir/identification/${gene}.txt $outdir/$gene/summary.txt + Rscript $dir/filter.r $PWD/mutationanalysis.txt $outdir/identification/${gene}.txt $outdir/$gene/mutationanalysis.txt + Rscript $dir/filter.r $PWD/mutationstats.txt $outdir/identification/${gene}.txt $outdir/$gene/mutationstats.txt + Rscript $dir/filter.r $PWD/hotspots.txt $outdir/identification/${gene}.txt $outdir/$gene/hotspots.txt + echo "done <br />" >> $output + + echo "Running R script on $gene..." >> $output + Rscript --verbose $dir/mutation_analysis.r $outdir/$gene/mutationstats.txt $outdir/$gene/summary.txt $outdir/$gene/ 2>&1 + echo "done <br />" >> $output + + echo "Running Python script..." >> $output + python $dir/mutation_analysis.py --mutationfile $outdir/$gene/mutationanalysis.txt --hotspotfile $outdir/$gene/hotspots.txt --output $outdir/$gene/hotspot_analysis.txt + echo "done <br />" >> $output + echo "Done with $gene <br />" >> $output + cut $outdir/$gene/mutations.txt -d, -f2,3,4 > $mutationtmp + cut $outdir/$gene/hotspot_analysis.txt -d, -f2,3,4 > $hotspottmp + cat $mutationtmp $hotspottmp > $tmp + paste $outdir/mutationandhotspot.txt -d, $tmp > $tmp2 + cat $tmp2 > $outdir/mutationandhotspot.txt +done + +Rscript --verbose $dir/mutation_analysis.r $PWD/mutationstats.txt $PWD/summary.txt $outdir/ 2>&1 +python $dir/mutation_analysis.py --mutationfile $PWD/mutationanalysis.txt --hotspotfile $PWD/hotspots.txt --output $outdir/hotspot_analysis.txt + +cut $outdir/mutations.txt -d, -f2,3,4 > $mutationtmp +cut $outdir/hotspot_analysis.txt -d, -f2,3,4 > $hotspottmp +cat $mutationtmp $hotspottmp > $tmp +paste $outdir/mutationandhotspot.txt -d, $tmp > $tmp2 +cat $tmp2 > $outdir/mutationandhotspot.txt + +cut $outdir/ca1/mutations.txt -d, -f1 > $mutationtmp +cut $outdir/ca1/hotspot_analysis.txt -d, -f1 > $hotspottmp +cat $mutationtmp $hotspottmp > $tmp +paste $tmp $outdir/mutationandhotspot.txt -d, > $tmp2 +cat $tmp2 | tr -s "," > $outdir/mutationandhotspot.txt + +ca_n=`cat $outdir/ca/n.txt` +ca1_n=`cat $outdir/ca1/n.txt` +ca2_n=`cat $outdir/ca2/n.txt` +cg_n=`cat $outdir/cg/n.txt` +cg1_n=`cat $outdir/cg1/n.txt` +cg2_n=`cat $outdir/cg2/n.txt` +cg3_n=`cat $outdir/cg3/n.txt` +cg4_n=`cat $outdir/cg4/n.txt` +cm_n=`cat $outdir/cm/n.txt` +#all_n=$((ca_n + cg_n + cm_n)) +all_n=`cat $outdir/n.txt` + + +echo "<html><table border='1'>" > $output +echo "<tr><th>info</th>" >> $output +echo "<th><a href='identification/ca.txt'>ca (N = $ca_n)</a></th>" >> $output +echo "<th><a href='identification/ca1.txt'>ca1 (N = $ca1_n)</a></th>" >> $output +echo "<th><a href='identification/ca2.txt'>ca2 (N = $ca2_n)</a></th>" >> $output +echo "<th><a href='identification/cg.txt'>cg (N = $cg_n)</a></th>" >> $output +echo "<th><a href='identification/cg1.txt'>cg1 (N = $cg1_n)</a></th>" >> $output +echo "<th><a href='identification/cg2.txt'>cg2 (N = $cg2_n)</a></th>" >> $output +echo "<th><a href='identification/cg3.txt'>cg3 (N = $cg3_n)</a></th>" >> $output +echo "<th><a href='identification/cg4.txt'>cg4 (N = $cg4_n)</a></th>" >> $output +echo "<th><a href='identification/cm.txt'>cm (N = $cm_n)</a></th>" >> $output +echo "<th>all (N = $all_n)</th></tr>" >> $output +while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz allx ally allz + do + echo "<tr><td>$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 +done < $outdir/mutationandhotspot.txt +echo "</table>" >> $output +echo "<a href='identification/unmatched.txt'>umatched</a><br />" >> $output + +Rscript $dir/piechart.r "${ca_n},${cg_n},${cm_n}" "IgA - ${ca_n},IgG - ${cg_n},IgM? - ${cm_n}" "Ig* (N = $all_n)" $outdir/all.png 2>&1 +Rscript $dir/piechart.r "${ca1_n},${ca2_n}" "IgA1 - ${ca1_n},IgA2 - ${ca2_n}" "IgA (N = $ca_n)" $outdir/ca.png 2>&1 +Rscript $dir/piechart.r "${cg1_n},${cg2_n},${cg3_n},${cg4_n}" "IgG1 - ${cg1_n},IgG2 - ${cg2_n},IgG3 - ${cg3_n},IgG4 - ${cg4_n}" "IgG (N = $cg_n)" $outdir/cg.png 2>&1 + +echo "<img src='all.png'/>" >> $output +echo "<img src='ca.png'/>" >> $output +echo "<img src='cg.png'/>" >> $output + +for gene in ${genes[@]} +do + echo "<table border='1'><caption>$gene transition table</caption>" >> $output + while IFS=, read from a c g t + do + echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output + done < $outdir/$gene/transitions.txt + echo "</table>" >> $output +done + +echo "<table border='1'><caption>All transition table</caption>" >> $output +while IFS=, read from a c g t + do + echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output +done < $outdir/transitions.txt +echo "</table>" >> $output + +echo "</html>" >> $output