Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 72:c787e79e8b90 draft

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Uploaded
author davidvanzessen
date Tue, 05 Feb 2019 03:26:41 -0500
parents 7b9481fa4a70
children
comparison
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71:2649a821162d 72:c787e79e8b90
70 fi 70 fi
71 71
72 echo "---------------- class identification ----------------" 72 echo "---------------- class identification ----------------"
73 echo "---------------- class identification ----------------<br />" >> $log 73 echo "---------------- class identification ----------------<br />" >> $log
74 74
75 python2 $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt 75 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
76 76
77 echo "---------------- merge_and_filter.r ----------------" 77 echo "---------------- merge_and_filter.r ----------------"
78 echo "---------------- merge_and_filter.r ----------------<br />" >> $log 78 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
79 79
80 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${filter_unique_count} ${class_filter} ${empty_region_filter} 2>&1 80 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${filter_unique_count} ${class_filter} ${empty_region_filter} 2>&1
196 Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir" 2>&1 196 Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir" 2>&1
197 197
198 echo "---------------- shm_csr.py ----------------" 198 echo "---------------- shm_csr.py ----------------"
199 echo "---------------- shm_csr.py ----------------<br />" >> $log 199 echo "---------------- shm_csr.py ----------------<br />" >> $log
200 200
201 python2 $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt 201 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt
202 202
203 echo "---------------- aa_histogram.r ----------------" 203 echo "---------------- aa_histogram.r ----------------"
204 echo "---------------- aa_histogram.r ----------------<br />" >> $log 204 echo "---------------- aa_histogram.r ----------------<br />" >> $log
205 205
206 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1 206 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1