Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 92:b869a126e2c4 draft

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Uploaded
author davidvanzessen
date Mon, 06 Jun 2016 08:26:54 -0400
parents f0e8dac22c6e
children e39176ccddc8
comparison
equal deleted inserted replaced
91:5e237c243088 92:b869a126e2c4
53 53
54 #BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin" 54 #BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin"
55 55
56 echo "${BLASTN_DIR}" 56 echo "${BLASTN_DIR}"
57 57
58 echo "identification ($method)"
59 echo "---------------- identification ($method) ----------------" 58 echo "---------------- identification ($method) ----------------"
60 echo "---------------- identification ($method) ----------------<br />" >> $output 59 echo "---------------- identification ($method) ----------------<br />" >> $output
61 60
62 if [[ "${method}" == "custom" ]] ; then 61 if [[ "${method}" == "custom" ]] ; then
63 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt 62 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
107 #Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1 106 #Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
108 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1 107 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
109 108
110 echo "<table border='1'>" > $outdir/base_overview.html 109 echo "<table border='1'>" > $outdir/base_overview.html
111 110
112 while read ID class seq A C G T 111 while IFS=$'\t' read ID class seq A C G T
113 do 112 do
114 echo "<tr><td>$ID</td><td>$seq</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html 113 echo "<tr><td>$ID</td><td>$seq</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html
115 done < $outdir/sequence_overview/ntoverview.txt 114 done < $outdir/sequence_overview/ntoverview.txt
116 115
117 116