Mercurial > repos > davidvanzessen > igblastn_immunerepertoire_igg

comparison combined.sh @ 3:6364030a16b8 draft

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author davidvanzessen
date Fri, 24 Jan 2014 04:02:33 -0500
parents 364b169ffb30
children 2f2544607ad6
comparison
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2:364b169ffb30 3:6364030a16b8
1 #!/bin/bash 1 #!/bin/bash
2
3 mkdir $PWD/igblastdatabase
4 unzip $dir/database.zip -d $PWD/igblastdatabase/
5
6 export IGDATA=$PWD/igblastdatabase/
7 2
8 clonalType=${@:(-3):1} 3 clonalType=${@:(-3):1}
9 html=${@:(-2):1} 4 html=${@:(-2):1}
10 imageDir=${@:(-1):1} 5 imageDir=${@:(-1):1}
11 dataCount=`expr $# - 3` 6 dataCount=`expr $# - 3`
13 dir="$(cd "$(dirname "$0")" && pwd)" 8 dir="$(cd "$(dirname "$0")" && pwd)"
14 array=("$@") 9 array=("$@")
15 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html 10 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html
16 echo "<tr><td>-----------------------------------</td></tr>" >> $html 11 echo "<tr><td>-----------------------------------</td></tr>" >> $html
17 12
18 13 mkdir $PWD/igblastdatabase
14 unzip $dir/database.zip -d $PWD/igblastdatabase/
15 export IGDATA=$PWD/igblastdatabase/
19 16
20 function blastAndParse { 17 function blastAndParse {
21 echo "<tr><td>Starting blast of sample $3 of patient $2</td></tr>" >> $html 18 echo "<tr><td>Starting blast of sample $3 of patient $2</td></tr>" >> $html
22 echo "$IGDATA/bin/igblastn -germline_db_V $IGDATA/database/human_gl_V -germline_db_J $IGDATA/database/human_gl_J -germline_db_D $IGDATA/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $IGDATA/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4" 19 echo "$IGDATA/bin/igblastn -germline_db_V $IGDATA/database/human_gl_V -germline_db_J $IGDATA/database/human_gl_J -germline_db_D $IGDATA/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $IGDATA/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4"
23 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 20 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