Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 29:80c4eebf7bc9 draft

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Uploaded
author davidvanzessen
date Thu, 08 Dec 2016 04:51:09 -0500
parents c0ecc31829bd
children 33a7c49d48a7
comparison
equal deleted inserted replaced
28:c0ecc31829bd 29:80c4eebf7bc9
185 185
186 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1 186 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
187 if [ -e "$outdir/aa_histogram_.png" ]; then 187 if [ -e "$outdir/aa_histogram_.png" ]; then
188 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png 188 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
189 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt 189 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
190 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
191 mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
192 mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
190 fi 193 fi
191 194
192 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE) 195 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
193 196
194 funcs=(sum mean median) 197 funcs=(sum mean median)
590 593
591 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output 594 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
592 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt' download='aa_id_mutations.txt' >Download</a></td></tr>" >> $output 595 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt' download='aa_id_mutations.txt' >Download</a></td></tr>" >> $output
593 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output 596 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output
594 597
598 echo "<tr><td>The data used to generate the aa mutation frequency plot</td><td><a href='aa_histogram_sum.txt' download='aa_histogram_sum.txt' >Download</a></td></tr>" >> $output
599 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGA</td><td><a href='aa_histogram_sum_IGA.txt' download='aa_histogram_sum_IGA.txt' >Download</a></td></tr>" >> $output
600 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGG</td><td><a href='aa_histogram_sum_IGG.txt' download='aa_histogram_sum_IGG.txt' >Download</a></td></tr>" >> $output
601 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGM</td><td><a href='aa_histogram_sum_IGM.txt' download='aa_histogram_sum_IGM.txt' >Download</a></td></tr>" >> $output
602 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGE</td><td><a href='aa_histogram_sum_IGE.txt' download='aa_histogram_sum_IGE.txt' >Download</a></td></tr>" >> $output
603
595 echo "<tr><td>Baseline PDF (<a href='http://selection.med.yale.edu/baseline/'>http://selection.med.yale.edu/baseline/</a>)</td><td><a href='baseline.pdf' download='baseline.pdf' >Download</a></td></tr>" >> $output 604 echo "<tr><td>Baseline PDF (<a href='http://selection.med.yale.edu/baseline/'>http://selection.med.yale.edu/baseline/</a>)</td><td><a href='baseline.pdf' download='baseline.pdf' >Download</a></td></tr>" >> $output
596 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output 605 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
597 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output 606 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
598 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output 607 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
599 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output 608 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output