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comparison complete.sh @ 58:a073fa12ef98 draft

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author davidvanzessen
date Fri, 18 Mar 2016 08:02:22 -0400
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57:16c7fc1c4bf8 58:a073fa12ef98
1 #!/bin/bash
2 set -e
3 inputFiles=($1)
4 outputDir=$3
5 outputFile=$3/index.html #$1
6 clonalType=$4
7 species=$5
8 locus=$6
9 filterproductive=$7
10 clonality_method=$8
11
12 html=$2
13 dir="$(cd "$(dirname "$0")" && pwd)"
14 array=("$@")
15 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html
16 echo "<tr><td>-----------------------------------</td></tr>" >> $html
17
18 #mkdir $PWD/igblastdatabase
19 #unzip $dir/database.zip -d $PWD/igblastdatabase/
20 #export IGDATA=$PWD/igblastdatabase/
21
22 id=""
23 forwardSlash="/"
24 mergerInput=()
25 echo "Before loop"
26 count=1
27 for current in "${inputFiles[@]}"
28 do
29 if [[ "$current" != *"$forwardSlash"* ]]; then
30 id="$current"
31 mergerInput+=($id)
32 count=1
33 continue
34 fi
35 echo "working on $current"
36 fileName=$(basename $current)
37 fileName="${fileName%.*}"
38 parsedFileName="$PWD/$fileName.parsed"
39 f=$(file $current)
40 zipType="Zip archive"
41 zxType="XZ compressed data"
42 if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"$zxType"* ]]
43 then
44 echo "<tr><td>Sample $count of patient $id is an archive file, using IMGT Loader</td></tr>" >> $html
45 fileName=$(basename $current)
46 bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName "${fileName}"
47 else
48 echo "<tr><td>Sample $count of patient $id is not a zip file so assuming fasta/fastq, using igBLASTn</td></tr>" >> $html
49 bash ${dir}/igblast/igblast.sh $current $species $locus $parsedFileName
50 fi
51 mergerInput+=($parsedFileName)
52 count=$((count+1))
53 done
54
55 echo "<tr><td>-----------------------------------</td></tr>" >> $html
56 echo "<tr><td>merging</td></tr>" >> $html
57
58 bash $dir/experimental_design/experimental_design.sh ${mergerInput[*]} $PWD/merged.txt
59
60 echo "<tr><td>done</td></tr>" >> $html
61 echo "<tr><td>-----------------------------------</td></tr>" >> $html
62 echo "<tr><td>plotting</td></tr>" >> $html
63
64 echo "after ED"
65
66 bash $dir/report_clonality/r_wrapper.sh $PWD/merged.txt $2 $outputDir $clonalType "$species" "$locus" $filterproductive $clonality_method
67