casp7=/projects/compbio/experiments/protein-predict/casp7/ projectdir=${casp7}constraints_v2/ TARGETS=T0283 T0288 T0289 T0290 T0291 T0292 T0293 T0295 T0296 T0297 T0298 T0299 T0300 T0301 T0302 T0303 T0304 T0305 T0306 T0307 T0308 T0309 T0311 T0312 T0313 T0314 T0315 T0316 T0317 T0318 T0319 T0321 T0322 T0323 T0324 T0325 T0326 T0327 T0328 T0329 T0330 T0331 T0332 T0335 T0338 T0339 T0340 T0341 T0342 T0345 T0346 T0347 T0348 T0349 T0350 T0351 T0353 T0354 T0356 T0357 T0358 T0359 T0360 T0361 T0362 T0363 T0364 T0365 T0367 T0368 T0369 T0370 T0371 T0372 T0373 T0374 T0375 T0376 T0378 T0379 T0380 T0381 T0382 T0383 T0384 T0385 TARGETS_1=T0283 T0288 T0289 T0290 T0291 T0292 T0293 T0295 T0296 T0297 T0298 T0299 T0300 T0301 T0302 T0303 T0304 T0305 T0306 T0307 T0308 T0309 T0311 T0312 T0313 T0314 T0315 T0316 T0317 T0318 T0319 T0321 T0322 T0323 T0324 T0325 T0326 T0327 T0328 T0329 T0330 T0331 T0332 TARGETS_2=T0335 T0338 T0339 T0340 T0341 T0342 T0345 T0346 T0347 T0348 T0349 T0350 T0351 T0353 T0354 T0356 T0357 T0358 T0359 T0360 T0361 T0362 T0363 T0364 T0365 T0367 T0368 T0369 T0370 T0371 T0372 T0373 T0374 T0375 T0376 T0378 T0379 T0380 T0381 T0382 T0383 T0384 T0385 TARGETS_TBM=T0283 T0288 T0289 T0290 T0291 T0292 T0293 T0295 T0297 T0298 T0299 T0301 T0302 T0303 T0304 T0305 T0306 T0308 T0311 T0312 T0313 T0315 T0316 T0317 T0318 T0321 T0322 T0323 T0324 T0325 T0326 T0327 T0328 T0329 T0330 T0331 T0332 T0335 T0338 T0339 T0340 T0341 T0342 T0345 T0346 T0347 T0348 T0349 T0351 T0354 T0356 T0357 T0358 T0359 T0360 T0362 T0363 T0364 T0365 T0367 T0368 T0369 T0370 T0371 T0372 T0373 T0374 T0375 T0376 T0378 T0379 T0380 T0381 T0383 T0384 T0385 TARGETS_HATBM=T0288 T0290 T0291 T0292 T0295 T0302 T0303 T0305 T0308 T0311 T0313 T0315 T0317 T0324 T0326 T0328 T0332 T0339 T0340 T0345 T0346 T0359 T0367 TARGETS_NOFM=T0283 T0288 T0289 T0290 T0291 T0292 T0293 T0295 T0297 T0298 T0299 T0301 T0302 T0303 T0305 T0306 T0308 T0311 T0312 T0313 T0315 T0317 T0318 T0322 T0323 T0324 T0325 T0326 T0327 T0328 T0329 T0330 T0331 T0332 T0335 T0338 T0339 T0340 T0341 T0342 T0345 T0346 T0349 T0351 T0354 T0357 T0358 T0359 T0360 T0362 T0363 T0364 T0365 T0367 T0368 T0369 T0370 T0371 T0372 T0373 T0374 T0375 T0376 T0378 T0379 T0380 T0381 T0383 T0384 T0385 copymakefiles: $(foreach target,${TARGETS},mkdir -p ${target}; \ cp Make.main ${target}/Makefile;\ perl -pi -e s/XTARGET/${target}/g ${target}/Makefile;) initialize: $(foreach target,${TARGETS},rm -rf ${target};) $(foreach target,${TARGETS},mkdir -p ${target}; \ cp Make.main ${target}/Makefile;\ perl -pi -e s/XTARGET/${target}/g ${target}/Makefile;) rm tocluster* fraction%: rm -rf tocluster.fraction$*.jobs $(foreach target,${TARGETS},echo "cd "${projectdir}${target}"; make fraction"$*".costfcn" >> tocluster.fraction$*.jobs;) length_fraction%: rm -rf tocluster.length_fraction$*.jobs $(foreach target,${TARGETS},echo "cd "${projectdir}${target}"; make length_fraction"$*".costfcn" >> tocluster.length_fraction$*.jobs;) all-radius-%: rm -rf tocluster.all-radius-$*.jobs $(foreach target,${TARGETS},echo "cd "${projectdir}${target}"; make constraint-all-radius-"$*".costfcn" >> tocluster.all-radius-$*.jobs;) optimized8-%: rm -rf tocluster.optimized8-$*.jobs $(foreach target,${TARGETS},echo "cd "${projectdir}${target}"; make optimized8-"$*".costfcn" >> tocluster.optimized8-$*.jobs;) kendallserver-%: cd CostFcnEval;./cfneval.pl -us "decoys/servers.evaluate."$*".rdb" > ../tocluster.$*.kendallservers.jobs kendall-%: cd CostFcnEval;./cfneval.pl -us "decoys/predictions.evaluate."$*".rdb" > ../tocluster.$*.kendall.jobs clean-allconstraints: $(foreach target,${TARGETS},cd ${projectdir}${target}; rm alignment_constraints-good-all-*.under;) clean-rdbs: $(foreach target,${TARGETS},cd ${casp7}${target}; rm decoys/predictions.evaluate.constraint-best*.rdb;) download_qa_files: $(foreach target,${TARGETS},cd ${projectdir}${target}; mkdir -p QA_634; wget -O QA_634/${target} -r --tries=10 "http://www.predictioncenter.org/casp/casp7/public/cgi-bin/text.cgi?file=RESULTS/QA/${target}QA634_1"; ) # WARNING: DO THIS ON BOTH TARGET SETS compute_correlations: $(foreach target,${TARGETS_1},cd ${projectdir}${target}/MQA;\ cat ${casp7}${target}/decoys/servers.evaluate.constraint-best.rdb | column name GDT real_cost cost backbone_only > GDT_OUR_REAL.clean; \ cat ${target} | grep -i "[:alpha:]" | gawk 'BEGIN{start=0;}{if (start==1) print $$1, $$2; if ($$1=="MODEL") start=1;}' > 634.clean; \ echo "OURSTART" > temp; \ cat GDT_OUR_REAL.clean >> temp; \ echo "SERVERSTART" >> temp; \ cat 634.clean >> temp; \ cat temp|gawk -f ../../scripts/mergeQA.awk|sort -n -k 3 -r|gawk -f ${projectdir}/scripts/norm.awk|gawk -f ${projectdir}/scripts/log_x.awk|gawk -f ${projectdir}/scripts/norm.awk > 634.done; \ cat 634.done|gawk -f ../../scripts/pearson.awk -v group=1 -v gdt=0 > pearson-real.634; \ cat 634.done|gawk -f ../../scripts/pearson.awk -v group=1 -v gdt=1 > pearson-gdt.634; \ cat 634.done|gawk -f ../../scripts/pearson.awk -v group=0 -v gdt=0 > pearson-real.OUR; \ cat 634.done|gawk -f ../../scripts/pearson.awk -v group=0 -v gdt=1 > pearson-gdt.OUR; \ cat 634.done|gawk -f ../../scripts/kendall.awk -v group=1 -v gdt=0 > kendall-real.634; \ cat 634.done|gawk -f ../../scripts/kendall.awk -v group=1 -v gdt=1 > kendall-gdt.634; \ cat 634.done|gawk -f ../../scripts/kendall.awk -v group=0 -v gdt=0 > kendall-real.OUR; \ cat 634.done|gawk -f ../../scripts/kendall.awk -v group=0 -v gdt=1 > kendall-gdt.OUR; \ rm -rf p;\ echo -n ${target} >> p; \ cat pearson-real.634|gawk '{printf(" %s ", $$1)}' >> p; \ cat pearson-gdt.634|gawk '{printf(" %s ", $$1)}' >> p; \ cat pearson-real.OUR|gawk '{printf(" %s ", $$1)}' >> p; \ cat pearson-gdt.OUR|gawk '{printf(" %s ", $$1)}' >> p; \ cat kendall-real.634|gawk '{printf(" %s ", $$1)}' >> p; \ cat kendall-gdt.634|gawk '{printf(" %s ", $$1)}' >> p; \ cat kendall-real.OUR|gawk '{printf(" %s ", $$1)}' >> p; \ cat kendall-gdt.OUR|gawk '{printf(" %s \n", $$1)}' >> p; ) compare_correlations: rm -rf ${projectdir}$/pearsons $(foreach target,${TARGETS},cd ${projectdir}${target}/MQA;\ cat p >> ${projectdir}/pearsons; ) cat ${projectdir}/pearsons|gawk -f ${projectdir}/scripts/compare-correlations.awk evalue-kendall: rm -rf ${projectdir}/best_evalues.dat $(foreach target,${TARGETS},cd ${casp7}${target}; echo -n ${target} >> ${projectdir}/best_evalues.dat; cat ${target}.best-scores.rdb|gawk 'BEGIN{l=0}{l++; if (l==3) {printf(" %s ", $$4)}}'>> ${projectdir}/best_evalues.dat; cat ${projectdir}CostFcnEval/runs/constraint-optimized8_bonus_nonc-1-real_cost-tau.rdb|grep ${target}|gawk '{print $$2}' >> ${projectdir}/best_evalues.dat; ) combine-constraints: $(foreach target,${TARGETS}, cd ${projectdir}${target}; make constraint-combined.costfcn;) adjust_weights: $(foreach target,${TARGETS},cd ${casp7}${target}; cat constraint-optimized8_bonus_nonc-1.costfcn | gawk -f ../constraints_v2/scripts/adjust_weights.awk > constraint-best.costfcn;)