Mercurial > repos > davidvanzessen > complete_immunerepertoire_igg

comparison complete.sh @ 7:a9053212a462 draft

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Uploaded
author davidvanzessen
date Mon, 05 Jan 2015 09:30:08 -0500
parents 8b46fca04595
children 1b356cbde361
comparison
equal deleted inserted replaced
6:8b46fca04595 7:a9053212a462
4 outputDir=$3 4 outputDir=$3
5 outputFile=$3/index.html #$1 5 outputFile=$3/index.html #$1
6 clonalType=$4 6 clonalType=$4
7 species=$5 7 species=$5
8 locus=$6 8 locus=$6
9 selection=$7 9 filterproductive=$7
10 10
11 html=$2 11 html=$2
12 dir="$(cd "$(dirname "$0")" && pwd)" 12 dir="$(cd "$(dirname "$0")" && pwd)"
13 array=("$@") 13 array=("$@")
14 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html 14 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html
21 function blastAndParse { 21 function blastAndParse {
22 echo "<tr><td>Starting blast of sample $3 of patient $2</td></tr>" >> $html 22 echo "<tr><td>Starting blast of sample $3 of patient $2</td></tr>" >> $html
23 echo "igblastn -germline_db_V $PWD/igblastdatabase/database/human_gl_V -germline_db_J $PWD/igblastdatabase/database/human_gl_J -germline_db_D $PWD/igblastdatabase/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $PWD/igblastdatabase/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4" 23 echo "igblastn -germline_db_V $PWD/igblastdatabase/database/human_gl_V -germline_db_J $PWD/igblastdatabase/database/human_gl_J -germline_db_D $PWD/igblastdatabase/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $PWD/igblastdatabase/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4"
24 /home/galaxy/galaxy/igblast/igblastn -germline_db_V $PWD/igblastdatabase/database/human_gl_V -germline_db_J $PWD/igblastdatabase/database/human_gl_J -germline_db_D $PWD/igblastdatabase/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $PWD/igblastdatabase/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4 24 /home/galaxy/galaxy/igblast/igblastn -germline_db_V $PWD/igblastdatabase/database/human_gl_V -germline_db_J $PWD/igblastdatabase/database/human_gl_J -germline_db_D $PWD/igblastdatabase/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $PWD/igblastdatabase/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4
25 echo "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html 25 echo "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html
26
27 echo "<tr><td>Starting parse of sample $3 of patient $2</td></tr>" >> $html 26 echo "<tr><td>Starting parse of sample $3 of patient $2</td></tr>" >> $html
28 perl $dir/igparse.pl $PWD/$4 0 | grep -v "D:" | cut -f2- > "$5" 27 perl $dir/igparse.pl $PWD/$4 0 | grep -v "D:" | cut -f2- > "$5"
29 echo "<tr><td>Finished parse of sample $3 of patient $2</td></tr>" >> $html 28 echo "<tr><td>Finished parse of sample $3 of patient $2</td></tr>" >> $html
30 } 29 }
31 30
32 function imgtConvert { 31 function imgtConvert {
33 echo "<tr><td>Starting imgt convert of sample $3 of patient $2</td></tr>" >> $html 32 echo "<tr><td>Starting imgt convert of sample $3 of patient $2</td></tr>" >> $html
34 bash $dir/imgt_loader.sh $1 $4 $5 33 bash $dir/imgt_loader.sh $1 $4 $5
35 echo "<tr><td>Finished conversion of sample $3 of patient $2</td></tr>" >> $html 34 echo "<tr><td>Finished conversion of sample $3 of patient $2</td></tr>" >> $html
36
37 } 35 }
38 36
39 id="" 37 id=""
40 forwardSlash="/" 38 forwardSlash="/"
41 mergerInput=() 39 mergerInput=()
80 echo "<tr><td>-----------------------------------</td></tr>" >> $html 78 echo "<tr><td>-----------------------------------</td></tr>" >> $html
81 echo "<tr><td>plotting</td></tr>" >> $html 79 echo "<tr><td>plotting</td></tr>" >> $html
82 80
83 echo "after ED" 81 echo "after ED"
84 82
85 if [ "$locus" == "igh" ] || [ "$locus" == "igk" ] || [ "$locus" == "igl" ]; then 83 $dir/r_wrapper.sh $PWD/merged.txt $2 $outputDir $clonalType $species $locus $filterproductive
86 bash $dir/r_wrapper_b.sh $PWD/merged.txt $2 $outputDir $clonalType $species $locus $selection
87 else
88 bash $dir/r_wrapper_t.sh $PWD/merged.txt $2 $outputDir $clonalType $species $locus $selection
89 fi
90 84
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