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comparison wrapper.sh @ 101:3cffb8a38bb1 draft

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author davidvanzessen
date Fri, 17 Jun 2016 08:31:20 -0400
parents ff5be711382b
children e6bc976760d4
comparison
equal deleted inserted replaced
100:ff5be711382b 101:3cffb8a38bb1
101 101
102 mkdir $outdir/new_IMGT_cm 102 mkdir $outdir/new_IMGT_cm
103 cp $outdir/new_IMGT/* $outdir/new_IMGT_cm 103 cp $outdir/new_IMGT/* $outdir/new_IMGT_cm
104 104
105 Rscript $dir/tmp/igat.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1 105 Rscript $dir/tmp/igat.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
106 Rscript $dir/tmp/igat.r $outdir/new_IMGT_ca/ $outdir/merged.txt "ca "2>&1 106 Rscript $dir/tmp/igat.r $outdir/new_IMGT_ca/ $outdir/merged.txt "ca" 2>&1
107 Rscript $dir/tmp/igat.r $outdir/new_IMGT_cg/ $outdir/merged.txt "cg "2>&1 107 Rscript $dir/tmp/igat.r $outdir/new_IMGT_cg/ $outdir/merged.txt "cg" 2>&1
108 Rscript $dir/tmp/igat.r $outdir/new_IMGT_cm/ $outdir/merged.txt "cm "2>&1 108 Rscript $dir/tmp/igat.r $outdir/new_IMGT_cm/ $outdir/merged.txt "cm" 2>&1
109 109
110 110
111 tmp="$PWD" 111 tmp="$PWD"
112 cd $outdir/new_IMGT/ #tar weirdness... 112 cd $outdir/new_IMGT/ #tar weirdness...
113 tar -cJf ../new_IMGT.txz * 113 tar -cJf ../new_IMGT.txz *
295 echo "</table>" >> $output 295 echo "</table>" >> $output
296 296
297 echo "</html>" >> $output 297 echo "</html>" >> $output
298 298
299 echo "---------------- baseline ----------------" 299 echo "---------------- baseline ----------------"
300 tmp="$PWD"
301
302 mkdir $outdir/baseline
303
304
305 mkdir $outdir/baseline/ca_cg_cm
306 cd $outdir/baseline/ca_cg_cm
300 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "ca_cg_cm" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt" 307 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "ca_cg_cm" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
308
309 mkdir $outdir/baseline/ca
310 cd $outdir/baseline/ca
301 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_ca.txz "ca" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_ca.pdf" "Sequence.ID" "$outdir/baseline_ca.txt" 311 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_ca.txz "ca" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_ca.pdf" "Sequence.ID" "$outdir/baseline_ca.txt"
312
313 mkdir $outdir/baseline/cg
314 cd $outdir/baseline/cg
302 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cg.txz "cg" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cg.pdf" "Sequence.ID" "$outdir/baseline_cg.txt" 315 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cg.txz "cg" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cg.pdf" "Sequence.ID" "$outdir/baseline_cg.txt"
316
317 mkdir $outdir/baseline/cm
318 cd $outdir/baseline/cm
303 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cm.txz "cm" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cm.pdf" "Sequence.ID" "$outdir/baseline_cm.txt" 319 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cm.txz "cm" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cm.pdf" "Sequence.ID" "$outdir/baseline_cm.txt"
320
321 cd $tmp
304 322
305 #optional output for naive 323 #optional output for naive
306 324
307 echo "---------------- naive_output.r ----------------" 325 echo "---------------- naive_output.r ----------------"
308 326