Mercurial > repos > davidvanzessen > igblastn_immunerepertoire_igg

comparison combined.sh @ 2:364b169ffb30 draft

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Uploaded
author davidvanzessen
date Thu, 23 Jan 2014 08:30:59 -0500
parents 7b0d9c107680
children 6364030a16b8
comparison
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1:7b0d9c107680 2:364b169ffb30
18 18
19 19
20 function blastAndParse { 20 function blastAndParse {
21 echo "<tr><td>Starting blast of sample $3 of patient $2</td></tr>" >> $html 21 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/$4" 22 echo "$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"
23 $IGDATA/bin/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 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 echo "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html 24 echo "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html
25 25
26 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
27 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
28 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