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0
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1 #!/bin/bash
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4
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2 set -e
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0
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3 dir="$(cd "$(dirname "$0")" && pwd)"
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4 input=$1
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19
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5 method=$2
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6 output=$3
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7 outdir=$4
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8 title=$5
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22
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9 include_fr1=$6
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34
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10 functionality=$7
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11 unique=$8
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69
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12 naive_output_ca=$9
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13 naive_output_cg=${10}
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14 naive_output_cm=${11}
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15 filter_unique=${12}
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16 class_filter=${13}
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0
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17 mkdir $outdir
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18
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55
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19 echo "---------------- read parameters ----------------"
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63
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20 echo "---------------- read parameters ----------------<br />" > $output
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55
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21
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22 echo "unpacking IMGT file"
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23
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89
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24
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25
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35
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26 type="`file $input`"
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27 if [[ "$type" == *"Zip archive"* ]] ; then
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28 echo "Zip archive"
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29 echo "unzip $input -d $PWD/files/"
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30 unzip $input -d $PWD/files/
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31 elif [[ "$type" == *"XZ compressed data"* ]] ; then
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32 echo "ZX archive"
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33 echo "tar -xJf $input -C $PWD/files/"
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34 mkdir -p $PWD/files/$title
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35 tar -xJf $input -C $PWD/files/$title
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36 fi
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37
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64
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38 cat `find $PWD/files/ -name "1_*"` > $PWD/summary.txt
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39 cat `find $PWD/files/ -name "3_*"` > $PWD/sequences.txt
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40 cat `find $PWD/files/ -name "5_*"` > $PWD/aa.txt
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41 cat `find $PWD/files/ -name "6_*"` > $PWD/junction.txt
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42 cat `find $PWD/files/ -name "7_*"` > $PWD/mutationanalysis.txt
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43 cat `find $PWD/files/ -name "8_*"` > $PWD/mutationstats.txt
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44 cat `find $PWD/files/ -name "10_*"` > $PWD/hotspots.txt
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45
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46 #cat $PWD/files/*/1_* > $PWD/summary.txt
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47 #cat $PWD/files/*/3_* > $PWD/sequences.txt
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48 #cat $PWD/files/*/5_* > $PWD/aa.txt
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49 #cat $PWD/files/*/6_* > $PWD/junction.txt
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50 #cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
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51 #cat $PWD/files/*/8_* > $PWD/mutationstats.txt
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52 #cat $PWD/files/*/10_* > $PWD/hotspots.txt
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3
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53
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26
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54 #BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin"
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19
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55
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56 echo "${BLASTN_DIR}"
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57
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89
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58 echo "---------------- identification ($method) ----------------"
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59 echo "---------------- identification ($method) ----------------<br />" >> $output
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60
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19
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61 if [[ "${method}" == "custom" ]] ; then
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62 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
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63 else
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64 ID_index=$(cat $PWD/summary.txt | grep -o -P ".+Sequence ID" | grep -o -P "\t" | wc -l)
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65 ID_index=$((ID_index+1))
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66 sequence_index=$(cat $PWD/summary.txt | grep -o -P ".+\tSequence" | grep -o -P "\t" | wc -l)
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67 sequence_index=$((sequence_index+1))
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68
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69 cat $PWD/summary.txt | tail -n+2 | cut -f ${ID_index},${sequence_index} | awk '{print ">" $1 "\n" $2}' > $PWD/sequences.fasta
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70
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71 echo -e "qseqid\tsseqid\tpident\tlength\tmismatch\tgapopen\tqstart\tqend\tsstart\tsend\tevalue\tbitscore" > $outdir/identified_genes.txt
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72 ${BLASTN_DIR}/blastn -task blastn -db $dir/subclass_definition.db -query $PWD/sequences.fasta -outfmt 6 >> $outdir/identified_genes.txt
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73 fi
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74
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55
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75 echo "---------------- merge_and_filter.r ----------------"
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63
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76 echo "---------------- merge_and_filter.r ----------------<br />" >> $output
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19
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77
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90
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78 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} 2>&1
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79
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98
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80 echo "---------------- creating new IMGT zip ----------------"
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95
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81 echo "---------------- creating new IMGT zip ----------------<br />" >> $output
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82
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83 mkdir $outdir/new_IMGT
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84
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85 cat `find $PWD/files/ -name "1_*"` > "$outdir/new_IMGT/1_Summary.txt"
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86 cat `find $PWD/files/ -name "2_*"` > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
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87 cat `find $PWD/files/ -name "3_*"` > "$outdir/new_IMGT/3_Nt-sequences.txt"
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88 cat `find $PWD/files/ -name "4_*"` > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
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89 cat `find $PWD/files/ -name "5_*"` > "$outdir/new_IMGT/5_AA-sequences.txt"
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90 cat `find $PWD/files/ -name "6_*"` > "$outdir/new_IMGT/6_Junction.txt"
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91 cat `find $PWD/files/ -name "7_*"` > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
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92 cat `find $PWD/files/ -name "8_*"` > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
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93 cat `find $PWD/files/ -name "9_*"` > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
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94 cat `find $PWD/files/ -name "10_*"` > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
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95
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99
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96 mkdir $outdir/new_IMGT_ca
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97 cp $outdir/new_IMGT/* $outdir/new_IMGT_ca
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98
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99 mkdir $outdir/new_IMGT_cg
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100 cp $outdir/new_IMGT/* $outdir/new_IMGT_cg
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101
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102 mkdir $outdir/new_IMGT_cm
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103 cp $outdir/new_IMGT/* $outdir/new_IMGT_cm
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104
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105 Rscript $dir/tmp/igat.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
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106 Rscript $dir/tmp/igat.r $outdir/new_IMGT_ca/ $outdir/merged.txt "ca "2>&1
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107 Rscript $dir/tmp/igat.r $outdir/new_IMGT_cg/ $outdir/merged.txt "cg "2>&1
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108 Rscript $dir/tmp/igat.r $outdir/new_IMGT_cm/ $outdir/merged.txt "cm "2>&1
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95
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109
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110
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111 tmp="$PWD"
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112 cd $outdir/new_IMGT/ #tar weirdness...
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113 tar -cJf ../new_IMGT.txz *
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114 cp $dir/tmp/IgAT.xlsm $outdir/new_IMGT/IgAT.xlsm
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115 zip -r ../IgAT.zip *
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116
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99
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117 cd $outdir/new_IMGT_ca/
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118 tar -cJf ../new_IMGT_ca.txz *
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119 cp $dir/tmp/IgAT.xlsm $outdir/new_IMGT_ca/IgAT.xlsm
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120 zip -r ../IgAT_ca.zip *
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121
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122 cd $outdir/new_IMGT_cg/
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123 tar -cJf ../new_IMGT_cg.txz *
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124 cp $dir/tmp/IgAT.xlsm $outdir/new_IMGT_cg/IgAT.xlsm
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125 zip -r ../IgAT_cg.zip *
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126
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127 cd $outdir/new_IMGT_cm/
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128 tar -cJf ../new_IMGT_cm.txz *
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129 cp $dir/tmp/IgAT.xlsm $outdir/new_IMGT_cm/IgAT.xlsm
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130 zip -r ../IgAT_cm.zip *
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131
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132 cd $tmp
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133
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134 echo "---------------- mutation_analysis.r ----------------"
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135 echo "---------------- mutation_analysis.r ----------------<br />" >> $output
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136
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137 classes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm,unmatched"
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4
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138 echo "R mutation analysis"
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82
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139 Rscript $dir/mutation_analysis.r $outdir/merged.txt $classes $outdir ${include_fr1} 2>&1
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140
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141
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142 echo "---------------- mutation_analysis.py ----------------"
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143 echo "---------------- mutation_analysis.py ----------------<br />" >> $output
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144
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82
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145 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $classes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt
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146
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147 echo "---------------- aa_histogram.r ----------------"
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148 echo "---------------- aa_histogram.r ----------------<br />" >> $output
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149
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150 Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png 2>&1
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4
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151
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152 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm)
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153
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154 funcs=(sum mean median)
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155
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82
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156 echo "---------------- sequence_overview.r ----------------"
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157 echo "---------------- sequence_overview.r ----------------" >> $output
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82
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158
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159 mkdir $outdir/sequence_overview
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160
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161 #Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
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100
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162 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
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163
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164 echo "<table border='1'>" > $outdir/base_overview.html
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165
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166 while IFS=$'\t' read ID class seq A C G T
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167 do
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168 echo "<tr><td>$ID</td><td>$seq</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html
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82
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169 done < $outdir/sequence_overview/ntoverview.txt
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170
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171
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172 echo "<html><center><h1>$title</h1></center>" > $output
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173
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174 #display the matched/unmatched for clearity
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175
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176 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
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177 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
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178 total_count=$((matched_count + unmatched_count))
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179 perc_count=$((unmatched_count / total_count * 100))
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180 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
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181 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
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182
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183 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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184 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
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185 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
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186
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187 echo "---------------- main tables ----------------"
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53
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188 for func in ${funcs[@]}
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4
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189 do
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190
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191 echo "---------------- $func table ----------------"
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192
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94
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193 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
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194
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195 echo "<table border='1' width='100%'><caption><h3><a href='data_${func}.txt'>${func} table</a></h3></caption>" >> $output
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196 echo "<tr><th>info</th>" >> $output
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53
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197 for gene in ${genes[@]}
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198 do
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199 tmp=`cat $outdir/${gene}_${func}_n.txt`
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200 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
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201 done
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78
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202
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203 tmp=`cat $outdir/unmatched_${func}_n.txt`
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79
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204 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th>" >> $output
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205 tmp=`cat $outdir/all_${func}_n.txt`
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89
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206 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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207
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78
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208 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz unx uny unz allx ally allz
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53
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209 do
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210 if [ "$name" == "FR S/R (ratio)" ] || [ "$name" == "CDR S/R (ratio)" ] ; then #meh
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211 echo "<tr><td>$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>" >> $output
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212 else
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213 echo "<tr><td>$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} (${cmz}%)</td><td>${unx}/${uny} (${unz}%)</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
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53
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214 fi
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94
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215 done < $outdir/data_${func}.txt
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216 echo "</table>" >> $output
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217 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
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53
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218 done
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219
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55
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220 echo "---------------- download links ----------------"
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221
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94
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222
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223 echo "<a href='unmatched.txt'>unmatched</a><br />" >> $output
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224 echo "<a href='motif_per_seq.txt'>motif per sequence</a><br />" >> $output
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225 echo "<a href='merged.txt'>all data</a><br />" >> $output
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226 echo "<a href='mutation_by_id.txt'>mutations by id</a><br />" >> $output
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227 echo "<a href='aa_id_mutations.txt'>AA mutations location by id</a><br />" >> $output
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228 echo "<a href='absent_aa_id.txt'>Absant AA locations by id</a><br />" >> $output
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77
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229 echo "<a href='sequence_overview/index.html'>Sequence Overview</a><br />" >> $output
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81
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230 echo "<a href='base_overview.html'>Base overview</a><br />" >> $output
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95
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231 echo "<a href='baseline.pdf'>Baseline PDF</a><br />" >> $output
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232 echo "<a href='baseline.txt'>Baseline Table</a><br />" >> $output
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99
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233 echo "<a href='baseline_ca.pdf'>Baseline ca PDF</a><br />" >> $output
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234 echo "<a href='baseline_ca.txt'>Baseline ca Table</a><br />" >> $output
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235 echo "<a href='baseline_cg.pdf'>Baseline cg PDF</a><br />" >> $output
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236 echo "<a href='baseline_cg.txt'>Baseline cg Table</a><br />" >> $output
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237 echo "<a href='baseline_cm.pdf'>Baseline cm PDF</a><br />" >> $output
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238 echo "<a href='baseline_cm.txt'>Baseline cm Table</a><br />" >> $output
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95
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239 echo "<a href='IgAT.zip'>IgAT zip</a><br />" >> $output
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99
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240 echo "<a href='IgAT_ca.zip'>IgAT ca zip</a><br />" >> $output
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241 echo "<a href='IgAT_cg.zip'>IgAT cg zip</a><br />" >> $output
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242 echo "<a href='IgAT_cm.zip'>IgAT cm zip</a><br />" >> $output
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243 echo "<a href='new_IMGT.txz'>Filtered IMGT zip</a><br />" >> $output
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244 echo "<a href='new_IMGT_ca.txz'>Filtered ca IMGT zip</a><br />" >> $output
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245 echo "<a href='new_IMGT_cg.txz'>Filtered cg IMGT zip</a><br />" >> $output
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246 echo "<a href='new_IMGT_cm.txz'>Filtered cm IMGT zip</a><br />" >> $output
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247
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2
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248
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55
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249 echo "---------------- images ----------------"
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250
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4
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251 echo "<img src='all.png'/><br />" >> $output
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26
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252 echo "<a href='all.txt'>download data</a><br />" >> $output
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4
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253 if [ -a $outdir/ca.png ]
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254 then
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255 echo "<img src='ca.png'/><br />" >> $output
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26
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256 echo "<a href='ca.txt'>download data</a><br />" >> $output
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4
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257 fi
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258 if [ -a $outdir/cg.png ]
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259 then
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260 echo "<img src='cg.png'/><br />" >> $output
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26
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261 echo "<a href='cg.txt'>download data</a><br />" >> $output
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4
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262 fi
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22
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263 if [ -a $outdir/scatter.png ]
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264 then
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265 echo "<img src='scatter.png'/><br />" >> $output
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26
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266 echo "<a href='scatter.txt'>download data</a><br />" >> $output
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267 fi
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49
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268 if [ -a $outdir/frequency_ranges.png ]
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269 then
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270 echo "<img src='frequency_ranges.png'/><br />" >> $output
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271 echo "<a href='frequency_ranges_classes.txt'>download class data</a><br />" >> $output
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272 echo "<a href='frequency_ranges_subclasses.txt'>download subclass data</a><br />" >> $output
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273 fi
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26
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274 if [ -a $outdir/aa_histogram.png ]
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275 then
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276 echo "<img src='aa_histogram.png'/><br />" >> $output
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277 echo "<a href='aa_histogram.txt'>download data</a><br />" >> $output
|
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22
|
278 fi
|
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2
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279
|
|
0
|
280 for gene in ${genes[@]}
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|
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281 do
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282 echo "<table border='1'><caption>$gene transition table</caption>" >> $output
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|
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283 while IFS=, read from a c g t
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284 do
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285 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
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53
|
286 done < $outdir/transitions_${gene}_sum.txt
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|
0
|
287 echo "</table>" >> $output
|
|
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288 done
|
|
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289
|
|
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290 echo "<table border='1'><caption>All transition table</caption>" >> $output
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|
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291 while IFS=, read from a c g t
|
|
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292 do
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293 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
53
|
294 done < $outdir/transitions_all_sum.txt
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0
|
295 echo "</table>" >> $output
|
|
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296
|
|
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297 echo "</html>" >> $output
|
|
2
|
298
|
|
95
|
299 echo "---------------- baseline ----------------"
|
|
99
|
300 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "ca_cg_cm" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
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301 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_ca.txz "ca" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_ca.pdf" "Sequence.ID" "$outdir/baseline_ca.txt"
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302 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cg.txz "cg" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cg.pdf" "Sequence.ID" "$outdir/baseline_cg.txt"
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303 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cm.txz "cm" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cm.pdf" "Sequence.ID" "$outdir/baseline_cm.txt"
|
|
47
|
304
|
|
|
305 #optional output for naive
|
|
|
306
|
|
82
|
307 echo "---------------- naive_output.r ----------------"
|
|
55
|
308
|
|
47
|
309 if [[ "$naive_output" != "None" ]]
|
|
|
310 then
|
|
55
|
311 echo "---------------- imgt_loader.r ----------------"
|
|
50
|
312 #python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output
|
|
80
|
313 Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt $outdir/loader_output.txt 2>&1
|
|
95
|
314
|
|
55
|
315 echo "---------------- naive_output.r ----------------"
|
|
81
|
316 Rscript $dir/naive_output.r $outdir/loader_output.txt $outdir/merged.txt ${naive_output_ca} ${naive_output_cg} ${naive_output_cm} $outdir/ntoverview.txt $outdir/ntsum.txt 2>&1
|
|
47
|
317 fi
|
|
|
318
|
|
81
|
319 echo "</table>" >> $outdir/base_overview.html
|
|
|
320
|
|
|
321 echo "---------------- Done! ----------------"
|
|
47
|
322
|
