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comparison wrapper.sh @ 1:faae21ba5c63 draft

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Uploaded
author davidvanzessen
date Tue, 25 Oct 2016 07:28:43 -0400
parents c33d93683a09
children e85fec274cde
comparison
equal deleted inserted replaced
0:c33d93683a09 1:faae21ba5c63
156 echo "---------------- shm_csr.r ----------------" 156 echo "---------------- shm_csr.r ----------------"
157 echo "---------------- shm_csr.r ----------------<br />" >> $log 157 echo "---------------- shm_csr.r ----------------<br />" >> $log
158 158
159 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,unmatched" 159 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,unmatched"
160 echo "R mutation analysis" 160 echo "R mutation analysis"
161 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${include_fr1} 2>&1 161 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
162 162
163 163
164 echo "---------------- shm_csr.py ----------------" 164 echo "---------------- shm_csr.py ----------------"
165 echo "---------------- shm_csr.py ----------------<br />" >> $log 165 echo "---------------- shm_csr.py ----------------<br />" >> $log
166 166
167 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt 167 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt
168 168
169 echo "---------------- aa_histogram.r ----------------" 169 echo "---------------- aa_histogram.r ----------------"
170 echo "---------------- aa_histogram.r ----------------<br />" >> $log 170 echo "---------------- aa_histogram.r ----------------<br />" >> $log
171 171
172 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM" $outdir/ 2>&1 172 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM" $outdir/ 2>&1
573 echo "No IGM sequences" > "$outdir/baseline_IGM.txt" 573 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
574 fi 574 fi
575 575
576 cd $tmp 576 cd $tmp
577 577
578 echo "Cleaning up *.RData files"
579 find $outdir/baseline -name "*.RData" -type f -delete
580
578 echo "---------------- naive_output.r ----------------" 581 echo "---------------- naive_output.r ----------------"
579 echo "---------------- naive_output.r ----------------<br />" >> $log 582 echo "---------------- naive_output.r ----------------<br />" >> $log
580 583
581 if [[ "$naive_output" != "None" ]] 584 if [[ "$naive_output" != "None" ]]
582 then 585 then