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53
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1 #!/bin/bash
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2 set -e
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3 inputFiles=($1)
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4 outputDir=$3
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5 outputFile=$3/index.html #$1
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6 clonalType=$4
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7 species=$5
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8 locus=$6
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9 filterproductive=$7
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10 clonality_method=$8
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11
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12 html=$2
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13 dir="$(cd "$(dirname "$0")" && pwd)"
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14 array=("$@")
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15 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html
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16 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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17
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18 #mkdir $PWD/igblastdatabase
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19 #unzip $dir/database.zip -d $PWD/igblastdatabase/
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20 #export IGDATA=$PWD/igblastdatabase/
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21
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22 echo "python: `which python`"
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23 echo "R: `which R`"
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24 echo "Rscript: `which Rscript`"
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25
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26 id=""
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27 forwardSlash="/"
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28 mergerInput=()
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29 echo "Before loop"
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30 count=1
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31 for current in "${inputFiles[@]}"
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32 do
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33 if [[ "$current" != *"$forwardSlash"* ]]; then
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34 id="$current"
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35 mergerInput+=($id)
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36 count=1
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37 continue
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38 fi
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39 echo "working on $current"
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40 fileName=$(basename $current)
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41 fileName="${fileName%.*}"
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42 parsedFileName="$PWD/$fileName.parsed"
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43 f=$(file $current)
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44 zipType="Zip archive"
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45 zxType="XZ compressed data"
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46 echo "filetype of ${id}: $f"
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47 if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"$zxType"* ]]
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48 then
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49 echo "<tr><td>Sample $count of patient $id is an archive file, using IMGT Loader</td></tr>" >> $html
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50 fileName=$(basename $current)
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51 bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName "${fileName}"
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52 else
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53 echo "<tr><td>Sample $count of patient $id is not a zip file so assuming fasta/fastq, using igBLASTn</td></tr>" >> $html
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54 bash ${dir}/igblast/igblast.sh $current "$species" $locus $parsedFileName
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55 fi
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56 mergerInput+=($parsedFileName)
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57 count=$((count+1))
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58 done
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59
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60 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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61 echo "<tr><td>merging</td></tr>" >> $html
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62
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63 bash $dir/experimental_design/experimental_design.sh ${mergerInput[*]} $PWD/merged.txt
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64
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65 echo "<tr><td>done</td></tr>" >> $html
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66 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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67 echo "<tr><td>plotting</td></tr>" >> $html
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68
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69 echo "after ED"
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70
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71 bash $dir/report_clonality/r_wrapper.sh $PWD/merged.txt $2 $outputDir $clonalType "$species" "$locus" $filterproductive $clonality_method
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72
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