Mercurial > repos > davidvanzessen > igblastn_immunerepertoire_igg

comparison combined.sh @ 4:2f2544607ad6 draft

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Uploaded
author davidvanzessen
date Fri, 24 Jan 2014 04:04:55 -0500
parents 6364030a16b8
children be7ed742f870
comparison
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3:6364030a16b8 4:2f2544607ad6
14 unzip $dir/database.zip -d $PWD/igblastdatabase/ 14 unzip $dir/database.zip -d $PWD/igblastdatabase/
15 export IGDATA=$PWD/igblastdatabase/ 15 export IGDATA=$PWD/igblastdatabase/
16 16
17 function blastAndParse { 17 function blastAndParse {
18 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>" >> $html
19 echo "$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" 19 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"
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 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
21 echo "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html 21 echo "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html
22 22
23 echo "<tr><td>Starting parse of sample $3 of patient $2</td></tr>" >> $html 23 echo "<tr><td>Starting parse of sample $3 of patient $2</td></tr>" >> $html
24 perl $dir/igparse.pl $PWD/$4 0 | grep -v "D:" | cut -f2- > $5 24 perl $dir/igparse.pl $PWD/$4 0 | grep -v "D:" | cut -f2- > $5