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1 #!/bin/bash
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2 dir="$(cd "$(dirname "$0")" && pwd)"
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3
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4 input=$1
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5 output=$2
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6 outdir=$3
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7 mkdir $outdir
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8
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9 unzip $input -d $PWD/files/ > $PWD/unziplog.log
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10 cat $PWD/files/*/1_* > $PWD/summary.txt
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11 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
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12 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
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13 cat $PWD/files/*/10_* > $PWD/hotspots.txt
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14
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15 mkdir $outdir/identification/
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16 python $dir/gene_identification.py --input $PWD/summary.txt --outdir $outdir/identification/
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17 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm)
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18 tmp=$PWD/tmp
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19 tmp2=$PWD/tmp2
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20 hotspottmp=$PWD/hotspottmp
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21 mutationtmp=$PWD/mutationtmp
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22 touch $outdir/mutationandhotspot.txt
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23 for gene in ${genes[@]}
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24 do
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25 echo "Running $gene <br />" >> $output
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26 mkdir $outdir/$gene
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27 echo "Filtering input..." >> $output
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28 Rscript $dir/filter.r $PWD/summary.txt $outdir/identification/${gene}.txt $outdir/$gene/summary.txt
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29 Rscript $dir/filter.r $PWD/mutationanalysis.txt $outdir/identification/${gene}.txt $outdir/$gene/mutationanalysis.txt
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30 Rscript $dir/filter.r $PWD/mutationstats.txt $outdir/identification/${gene}.txt $outdir/$gene/mutationstats.txt
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31 Rscript $dir/filter.r $PWD/hotspots.txt $outdir/identification/${gene}.txt $outdir/$gene/hotspots.txt
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32 echo "done <br />" >> $output
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33
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34 echo "Running R script on $gene..." >> $output
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35 Rscript --verbose $dir/mutation_analysis.r $outdir/$gene/mutationstats.txt $outdir/$gene/summary.txt $outdir/$gene/ 2>&1
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36 echo "done <br />" >> $output
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37
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38 echo "Running Python script..." >> $output
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39 python $dir/mutation_analysis.py --mutationfile $outdir/$gene/mutationanalysis.txt --hotspotfile $outdir/$gene/hotspots.txt --output $outdir/$gene/hotspot_analysis.txt
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40 echo "done <br />" >> $output
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41 echo "Done with $gene <br />" >> $output
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42 cut $outdir/$gene/mutations.txt -d, -f2,3,4 > $mutationtmp
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43 cut $outdir/$gene/hotspot_analysis.txt -d, -f2,3,4 > $hotspottmp
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44 cat $mutationtmp $hotspottmp > $tmp
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45 paste $outdir/mutationandhotspot.txt -d, $tmp > $tmp2
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46 cat $tmp2 > $outdir/mutationandhotspot.txt
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47 done
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48
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49 Rscript --verbose $dir/mutation_analysis.r $PWD/mutationstats.txt $PWD/summary.txt $outdir/ 2>&1
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50 python $dir/mutation_analysis.py --mutationfile $PWD/mutationanalysis.txt --hotspotfile $PWD/hotspots.txt --output $outdir/hotspot_analysis.txt
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51
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52 cut $outdir/mutations.txt -d, -f2,3,4 > $mutationtmp
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53 cut $outdir/hotspot_analysis.txt -d, -f2,3,4 > $hotspottmp
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54 cat $mutationtmp $hotspottmp > $tmp
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55 paste $outdir/mutationandhotspot.txt -d, $tmp > $tmp2
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56 cat $tmp2 > $outdir/mutationandhotspot.txt
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57
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58 cut $outdir/ca1/mutations.txt -d, -f1 > $mutationtmp
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59 cut $outdir/ca1/hotspot_analysis.txt -d, -f1 > $hotspottmp
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60 cat $mutationtmp $hotspottmp > $tmp
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61 paste $tmp $outdir/mutationandhotspot.txt -d, > $tmp2
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62 cat $tmp2 | tr -s "," > $outdir/mutationandhotspot.txt
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63
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64 ca_n=`cat $outdir/ca/n.txt`
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65 ca1_n=`cat $outdir/ca1/n.txt`
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66 ca2_n=`cat $outdir/ca2/n.txt`
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67 cg_n=`cat $outdir/cg/n.txt`
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68 cg1_n=`cat $outdir/cg1/n.txt`
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69 cg2_n=`cat $outdir/cg2/n.txt`
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70 cg3_n=`cat $outdir/cg3/n.txt`
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71 cg4_n=`cat $outdir/cg4/n.txt`
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72 cm_n=`cat $outdir/cm/n.txt`
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73 #all_n=$((ca_n + cg_n + cm_n))
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74 all_n=`cat $outdir/n.txt`
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75
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76
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77 echo "<html><table border='1'>" > $output
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78 echo "<tr><th>info</th>" >> $output
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79 echo "<th><a href='identification/ca.txt'>ca (N = $ca_n)</a></th>" >> $output
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80 echo "<th><a href='identification/ca1.txt'>ca1 (N = $ca1_n)</a></th>" >> $output
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81 echo "<th><a href='identification/ca2.txt'>ca2 (N = $ca2_n)</a></th>" >> $output
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82 echo "<th><a href='identification/cg.txt'>cg (N = $cg_n)</a></th>" >> $output
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83 echo "<th><a href='identification/cg1.txt'>cg1 (N = $cg1_n)</a></th>" >> $output
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84 echo "<th><a href='identification/cg2.txt'>cg2 (N = $cg2_n)</a></th>" >> $output
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85 echo "<th><a href='identification/cg3.txt'>cg3 (N = $cg3_n)</a></th>" >> $output
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86 echo "<th><a href='identification/cg4.txt'>cg4 (N = $cg4_n)</a></th>" >> $output
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87 echo "<th><a href='identification/cm.txt'>cm (N = $cm_n)</a></th>" >> $output
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88 echo "<th>all (N = $all_n)</th></tr>" >> $output
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89 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz allx ally allz
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90 do
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91 echo "<tr><td>$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
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92 done < $outdir/mutationandhotspot.txt
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93 echo "</table>" >> $output
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94 echo "<a href='identification/unmatched.txt'>umatched</a><br />" >> $output
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95
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96 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
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97 Rscript $dir/piechart.r "${ca1_n},${ca2_n}" "IgA1 - ${ca1_n},IgA2 - ${ca2_n}" "IgA (N = $ca_n)" $outdir/ca.png 2>&1
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98 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
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99
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100 echo "<img src='all.png'/>" >> $output
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101 echo "<img src='ca.png'/>" >> $output
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102 echo "<img src='cg.png'/>" >> $output
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103
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104 for gene in ${genes[@]}
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105 do
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106 echo "<table border='1'><caption>$gene transition table</caption>" >> $output
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107 while IFS=, read from a c g t
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108 do
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109 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
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110 done < $outdir/$gene/transitions.txt
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111 echo "</table>" >> $output
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112 done
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113
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114 echo "<table border='1'><caption>All transition table</caption>" >> $output
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115 while IFS=, read from a c g t
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116 do
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117 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
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118 done < $outdir/transitions.txt
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119 echo "</table>" >> $output
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120
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121 echo "</html>" >> $output
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