Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 2:2f4298673519 draft

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Uploaded
author davidvanzessen
date Wed, 10 Sep 2014 10:33:29 -0400
parents 856b5b718d21
children a0b27058dcac
comparison
equal deleted inserted replaced
1:856b5b718d21 2:2f4298673519
10 unzip $input -d $PWD/files/ > $PWD/unziplog.log 10 unzip $input -d $PWD/files/ > $PWD/unziplog.log
11 cat $PWD/files/*/1_* > $PWD/summary.txt 11 cat $PWD/files/*/1_* > $PWD/summary.txt
12 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt 12 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
13 cat $PWD/files/*/8_* > $PWD/mutationstats.txt 13 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
14 cat $PWD/files/*/10_* > $PWD/hotspots.txt 14 cat $PWD/files/*/10_* > $PWD/hotspots.txt
15 cp $dir/HS12RSS.txt $outdir/
16 cp $dir/HS23RSS.txt $outdir/
15 17
16 mkdir $outdir/identification/ 18 mkdir $outdir/identification/
17 python $dir/gene_identification.py --input $PWD/summary.txt --outdir $outdir/identification/ 19 python $dir/gene_identification.py --input $PWD/summary.txt --outdir $outdir/identification/
18 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm) 20 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm)
19 tmp=$PWD/tmp 21 tmp=$PWD/tmp
23 touch $outdir/mutationandhotspot.txt 25 touch $outdir/mutationandhotspot.txt
24 for gene in ${genes[@]} 26 for gene in ${genes[@]}
25 do 27 do
26 echo "Running $gene <br />" >> $output 28 echo "Running $gene <br />" >> $output
27 mkdir $outdir/$gene 29 mkdir $outdir/$gene
30 cp $dir/HS12RSS.txt $outdir/$gene/
31 cp $dir/HS23RSS.txt $outdir/$gene/
28 echo "Filtering input..." >> $output 32 echo "Filtering input..." >> $output
29 Rscript $dir/filter.r $PWD/summary.txt $outdir/identification/${gene}.txt $outdir/$gene/summary.txt 33 Rscript $dir/filter.r $PWD/summary.txt $outdir/identification/${gene}.txt $outdir/$gene/summary.txt
30 Rscript $dir/filter.r $PWD/mutationanalysis.txt $outdir/identification/${gene}.txt $outdir/$gene/mutationanalysis.txt 34 Rscript $dir/filter.r $PWD/mutationanalysis.txt $outdir/identification/${gene}.txt $outdir/$gene/mutationanalysis.txt
31 Rscript $dir/filter.r $PWD/mutationstats.txt $outdir/identification/${gene}.txt $outdir/$gene/mutationstats.txt 35 Rscript $dir/filter.r $PWD/mutationstats.txt $outdir/identification/${gene}.txt $outdir/$gene/mutationstats.txt
32 Rscript $dir/filter.r $PWD/hotspots.txt $outdir/identification/${gene}.txt $outdir/$gene/hotspots.txt 36 Rscript $dir/filter.r $PWD/hotspots.txt $outdir/identification/${gene}.txt $outdir/$gene/hotspots.txt
43 cut $outdir/$gene/mutations.txt -d, -f2,3,4 > $mutationtmp 47 cut $outdir/$gene/mutations.txt -d, -f2,3,4 > $mutationtmp
44 cut $outdir/$gene/hotspot_analysis.txt -d, -f2,3,4 > $hotspottmp 48 cut $outdir/$gene/hotspot_analysis.txt -d, -f2,3,4 > $hotspottmp
45 cat $mutationtmp $hotspottmp > $tmp 49 cat $mutationtmp $hotspottmp > $tmp
46 paste $outdir/mutationandhotspot.txt -d, $tmp > $tmp2 50 paste $outdir/mutationandhotspot.txt -d, $tmp > $tmp2
47 cat $tmp2 > $outdir/mutationandhotspot.txt 51 cat $tmp2 > $outdir/mutationandhotspot.txt
52 rm $outdir/$gene/HS12RSS.txt
53 rm $outdir/$gene/HS23RSS.txt
48 done 54 done
49 55
50 Rscript --verbose $dir/mutation_analysis.r $PWD/mutationstats.txt $PWD/summary.txt $outdir/ 2>&1 56 Rscript --verbose $dir/mutation_analysis.r $PWD/mutationstats.txt $PWD/summary.txt $outdir/ 2>&1
51 python $dir/mutation_analysis.py --mutationfile $PWD/mutationanalysis.txt --hotspotfile $PWD/hotspots.txt --output $outdir/hotspot_analysis.txt 57 python $dir/mutation_analysis.py --mutationfile $PWD/mutationanalysis.txt --hotspotfile $PWD/hotspots.txt --output $outdir/hotspot_analysis.txt
52 58
96 102
97 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>&1 103 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
98 Rscript $dir/piechart.r "${ca1_n},${ca2_n}" "IgA1 - ${ca1_n},IgA2 - ${ca2_n}" "IgA (N = $ca_n)" $outdir/ca.png 2>&1 104 Rscript $dir/piechart.r "${ca1_n},${ca2_n}" "IgA1 - ${ca1_n},IgA2 - ${ca2_n}" "IgA (N = $ca_n)" $outdir/ca.png 2>&1
99 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>&1 105 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
100 106
107 $dir/seqlogo -t "HS12RSS" -w 20 -h 5 -p -a -c -n -F PNG -f $outdir/weblogo_in_rs12.txt > $outdir/HS12.png 2>&1
108 $dir/seqlogo -t "HS23RSS" -w 20 -h 5 -p -a -c -n -F PNG -f $outdir/weblogo_in_rs23.txt > $outdir/HS23.png 2>&1
109
110
101 echo "<img src='all.png'/>" >> $output 111 echo "<img src='all.png'/>" >> $output
102 echo "<img src='ca.png'/>" >> $output 112 echo "<img src='ca.png'/>" >> $output
103 echo "<img src='cg.png'/>" >> $output 113 echo "<img src='cg.png'/>" >> $output
114
115 echo "<img src='HS12.png'/>" >> $output
116 echo "<img src='HS23.png'/>" >> $output
104 117
105 for gene in ${genes[@]} 118 for gene in ${genes[@]}
106 do 119 do
107 echo "<table border='1'><caption>$gene transition table</caption>" >> $output 120 echo "<table border='1'><caption>$gene transition table</caption>" >> $output
108 while IFS=, read from a c g t 121 while IFS=, read from a c g t
118 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output 131 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
119 done < $outdir/transitions.txt 132 done < $outdir/transitions.txt
120 echo "</table>" >> $output 133 echo "</table>" >> $output
121 134
122 echo "</html>" >> $output 135 echo "</html>" >> $output
136
137 #rm $outdir/HS12RSS.txt
138 #rm $outdir/HS23RSS.txt