# HMMER's test suite, in sqc command format # # See the ../easel/devkit/sqc script for documentation of sqc. # # Usage: # sqc testsuite.sqc # Example: # cd build-debug # sqc 1 ../testsuite/valgrind.sqc . .. # # level 1 = the standard test suite # level 2 = (currently nothing) # level 3 = valgrind tests # # Remember, sqc does three types of file substitution on this file: # @foo@ = executables in the build directory => top_builddir/foo # !foo! = data files in the source directory => top_srcdir/foo # %FOO% = tmp files, created, managed, cleaned up by sqc itself # ################################################################ # Unit test drivers for each .c file ################################################################ 1 exercise hmmer @src/hmmer_utest@ 1 exercise build @src/build_utest@ 1 exercise generic_fwdback @src/generic_fwdback_utest@ 1 exercise generic_msv @src/generic_msv_utest@ 1 exercise generic_stotrace @src/generic_stotrace_utest@ 1 exercise generic_viterbi @src/generic_viterbi_utest@ 1 exercise hmmd_search_status @src/hmmd_search_status_utest@ 1 exercise logsum @src/logsum_utest@ 1 exercise modelconfig @src/modelconfig_utest@ 1 exercise seqmodel @src/seqmodel_utest@ 1 exercise p7_alidisplay @src/p7_alidisplay_utest@ 1 exercise p7_bg @src/p7_bg_utest@ 1 exercise p7_domain @src/p7_domain_utest@ 1 exercise p7_gmx @src/p7_gmx_utest@ 1 exercise p7_hit @src/p7_hit_utest@ 1 exercise p7_hmm @src/p7_hmm_utest@ 1 exercise p7_hmmfile @src/p7_hmmfile_utest@ 1 exercise p7_hmmd_search_stats @src/p7_hmmd_search_stats_utest@ 1 exercise p7_profile @src/p7_profile_utest@ 1 exercise p7_tophits @src/p7_tophits_utest@ 1 exercise p7_trace @src/p7_trace_utest@ 1 exercise p7_scoredata @src/p7_scoredata_utest@ 1 exercise decoding @src/impl/decoding_utest@ 1 exercise fwdback @src/impl/fwdback_utest@ 1 exercise io @src/impl/io_utest@ 1 exercise msvfilter @src/impl/msvfilter_utest@ 1 exercise null2 @src/impl/null2_utest@ 1 exercise optacc @src/impl/optacc_utest@ 1 exercise stotrace @src/impl/stotrace_utest@ 1 exercise vitfilter @src/impl/vitfilter_utest@ 1 exercise hmmpgmd2msa @src/hmmpgmd2msa_utest@ !testsuite/Caudal_act.hmm! # Still to come, unit tests for # emit.c # errors.c # evalues.c # eweight.c # heatmap.c # hmmer.c # island.c # modelstats.c # mpisupport.c (MPI testing needs to be handled specially) # p7_bg.c # p7_domaindef.c # p7_prior.c # p7_spensemble.c ################################################################ # Option tests ################################################################ # Prep a press'ed "minifam" that's used here and also in some integration tests, # and extract an individual 'typical' model Caudal_act. 1 prep Caudal @easel/miniapps/esl-afetch@ !testsuite/minifam! Caudal_act > %CAUDAL.STO% 1 prep hmm @src/hmmbuild@ %CAUDAL.HMM% %CAUDAL.STO% 1 prep minifam @src/hmmbuild@ %MINIFAM.HMM% !testsuite/minifam! 1 prep minifam_press @src/hmmpress@ %MINIFAM.HMM% # hmmalign xxxxxxxxxxxxxxxxxxxx 1 prep testseq @src/hmmemit@ -p --unilocal -L0 -N 4 --seed 42 !testsuite/Caudal_act.hmm! > %TESTSEQ% 1 exercise hmmalign @src/hmmalign@ !testsuite/Caudal_act.hmm! %TESTSEQ% 1 exercise hmmalign/-h @src/hmmalign@ -h 1 exercise hmmalign/-o @src/hmmalign@ -o /dev/null !testsuite/Caudal_act.hmm! %TESTSEQ% 1 exercise hmmalign/--mapali @src/hmmalign@ --mapali !testsuite/Caudal_act.sto! !testsuite/Caudal_act.hmm! %TESTSEQ% 1 exercise hmmalign/--trim @src/hmmalign@ --trim !testsuite/Caudal_act.hmm! %TESTSEQ% 1 exercise hmmalign/--amino @src/hmmalign@ --amino !testsuite/Caudal_act.hmm! %TESTSEQ% 1 exercise hmmalign/--informat @src/hmmalign@ --informat fasta !testsuite/Caudal_act.hmm! %TESTSEQ% 1 exercise hmmalign/--outformat @src/hmmalign@ --outformat a2m !testsuite/Caudal_act.hmm! %TESTSEQ% # hmmbuild xxxxxxxxxxxxxxxxxxxx 1 exercise hmmbuild @src/hmmbuild@ --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/-h @src/hmmbuild@ -h 1 exercise build/-n @src/hmmbuild@ -n foo --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/-o @src/hmmbuild@ -o %HMMBUILD.out% --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/-O @src/hmmbuild@ -O %HMMBUILD.sto% --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--amino @src/hmmbuild@ --amino --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/M1.sto! 1 exercise build/--dna @src/hmmbuild@ --dna --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/M1.sto! 1 exercise build/--rna @src/hmmbuild@ --rna --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/M1.sto! 1 exercise build/--fast @src/hmmbuild@ --fast --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--hand @src/hmmbuild@ --hand --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--symfrac @src/hmmbuild@ --symfrac 1.0 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--fragthresh @src/hmmbuild@ --fragthresh 0.4 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--wpb @src/hmmbuild@ --wpb --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--wgsc @src/hmmbuild@ --wgsc --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--wblosum @src/hmmbuild@ --wblosum --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--wnone @src/hmmbuild@ --wnone --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! # --wgiven not tested 1 exercise build/--wid @src/hmmbuild@ --wblosum --wid 0.5 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--eent @src/hmmbuild@ --eent --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--eclust @src/hmmbuild@ --eclust --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--enone @src/hmmbuild@ --enone --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--eset @src/hmmbuild@ --eset 1.0 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--ere @src/hmmbuild@ --eent --ere 0.55 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--esigma @src/hmmbuild@ --eent --esigma 44.0 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--eid @src/hmmbuild@ --eclust --eid 0.60 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--pnone @src/hmmbuild@ --pnone --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--plaplace @src/hmmbuild@ --plaplace --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--EmL @src/hmmbuild@ --EmL 100 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--EmN @src/hmmbuild@ --EmN 250 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--EvL @src/hmmbuild@ --EvL 100 --EmL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--EvN @src/hmmbuild@ --EvN 250 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--EfL @src/hmmbuild@ --EfL 100 --EmL 10 --EvL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--EfN @src/hmmbuild@ --EfN 250 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--Eft @src/hmmbuild@ --Eft 0.045 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--informat @src/hmmbuild@ --informat stockholm --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1 exercise build/--seed @src/hmmbuild@ --seed 42 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! # hmmsearch xxxxxxxxxxxxxxxxxxxx 1 prep rnddb @easel/miniapps/esl-shuffle@ -G --amino -L 100 -N 2 -o %RNDDB% 1 exercise search @src/hmmsearch@ !tutorial/globins4.hmm! %RNDDB% 1 exercise search/-h @src/hmmsearch@ -h 1 exercise search/-o @src/hmmsearch@ -o %HMMSEARCH.out% !tutorial/globins4.hmm! %RNDDB% 1 exercise search/-A @src/hmmsearch@ -A %HMMSEARCH.sto% !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--tblout @src/hmmsearch@ --tblout %HMMSEARCH.tbl% !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--domtblout @src/hmmsearch@ --domtblout %HMMSEARCH.dtbl% !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--pfamtblout @src/hmmsearch@ --pfamtblout %HMMSEARCH.dtbl% !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--acc @src/hmmsearch@ --acc !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--noali @src/hmmsearch@ --noali !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--notextw @src/hmmsearch@ --notextw !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--textw @src/hmmsearch@ --textw 256 !tutorial/globins4.hmm! %RNDDB% 1 exercise search/-E @src/hmmsearch@ -E 0.01 !tutorial/globins4.hmm! %RNDDB% 1 exercise search/-T @src/hmmsearch@ -T 20 !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--domE @src/hmmsearch@ --domE 0.01 !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--domT @src/hmmsearch@ --domT 20 !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--incE @src/hmmsearch@ --incE 0.01 !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--incT @src/hmmsearch@ --incT 20 !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--incdomE @src/hmmsearch@ --incdomE 0.01 !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--incdomT @src/hmmsearch@ --incdomT 20 !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--cut_ga @src/hmmsearch@ --cut_ga !tutorial/fn3.hmm! %RNDDB% 1 exercise search/--cut_nc @src/hmmsearch@ --cut_nc !tutorial/fn3.hmm! %RNDDB% 1 exercise search/--cut_tc @src/hmmsearch@ --cut_tc !tutorial/fn3.hmm! %RNDDB% 1 exercise search/--max @src/hmmsearch@ --max !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--F1 @src/hmmsearch@ --F1 0.03 !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--F2 @src/hmmsearch@ --F2 0.002 !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--F3 @src/hmmsearch@ --F3 0.0002 !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--nobias @src/hmmsearch@ --nobias !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--nonull2 @src/hmmsearch@ --nonull2 !tutorial/globins4.hmm! %RNDDB% 1 exercise search/-Z @src/hmmsearch@ -Z 45000000 !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--domZ @src/hmmsearch@ --domZ 45000000 !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--seed @src/hmmsearch@ --seed 42 !tutorial/globins4.hmm! %RNDDB% 1 exercise search/--tformat @src/hmmsearch@ --tformat fasta !tutorial/globins4.hmm! %RNDDB% # --cpu: threads only # --mpi: MPI only # hmmscan xxxxxxxxxxxxxxxxxxxx 1 exercise hmmscan @src/hmmscan@ %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/-h @src/hmmscan@ -h 1 exercise scan/-o @src/hmmscan@ -o %SCAN.out% %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--tblout @src/hmmscan@ --tblout %SCAN.tbl% %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--domtblout @src/hmmscan@ --domtblout %SCAN.dtbl% %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--pfamtblout @src/hmmscan@ --pfamtblout %SCAN.ptbl% %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--acc @src/hmmscan@ --acc %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--noali @src/hmmscan@ --noali %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--notextw @src/hmmscan@ --notextw %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--textw @src/hmmscan@ --textw 120 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/-E @src/hmmscan@ -E 0.01 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/-T @src/hmmscan@ -T 20 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--domE @src/hmmscan@ --domE 0.01 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--domT @src/hmmscan@ --domT 20 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--incE @src/hmmscan@ --incE 0.01 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--incT @src/hmmscan@ --incT 20 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--incdomE @src/hmmscan@ --incdomE 0.01 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--incdomT @src/hmmscan@ --incdomT 20 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--incdomT @src/hmmscan@ --incdomT 20 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--cut_ga @src/hmmscan@ --cut_ga %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--cut_nc @src/hmmscan@ --cut_nc %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--cut_tc @src/hmmscan@ --cut_tc %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--max @src/hmmscan@ --max %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--F1 @src/hmmscan@ --F1 0.03 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--F2 @src/hmmscan@ --F2 0.002 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--F3 @src/hmmscan@ --F3 0.0002 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--nobias @src/hmmscan@ --nobias %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--nonull2 @src/hmmscan@ --nonull2 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/-Z @src/hmmscan@ -Z 45000000 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--domZ @src/hmmscan@ --domZ 45000000 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--seed @src/hmmscan@ --seed 42 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--qformat @src/hmmscan@ --qformat fasta %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1 exercise scan/--cpu @src/hmmscan@ --cpu 2 %MINIFAM.HMM% !tutorial/HBB_HUMAN! # jackhmmer xxxxxxxxxxxxxxxxxxxx 1 exercise jackhmmer @src/jackhmmer@ --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/-h @src/jackhmmer@ -h 1 exercise j/-N @src/jackhmmer@ -N 2 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/-o @src/jackhmmer@ -o %JHMMER.out% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/-A @src/jackhmmer@ -A %JHMMER.sto% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--tblout @src/jackhmmer@ --tblout %JHMMER.tbl% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--domtblout @src/jackhmmer@ --domtblout %JHMMER.dtbl% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--chkhmm @src/jackhmmer@ --chkhmm %JHMMER.ch% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--chkali @src/jackhmmer@ --chkali %JHMMER.ca% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--acc @src/jackhmmer@ --acc --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--noali @src/jackhmmer@ --noali --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--notextw @src/jackhmmer@ --notextw --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--textw @src/jackhmmer@ --textw 256 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--popen @src/jackhmmer@ --popen 0.4 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--pextend @src/jackhmmer@ --pextend 0.6 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--mxfile @src/jackhmmer@ --mxfile !easel/formats/BLOSUM62! --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/-E @src/jackhmmer@ -E 0.01 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/-T @src/jackhmmer@ -T 20 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--domE @src/jackhmmer@ --domE 0.01 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--domT @src/jackhmmer@ --domT 20 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--incE @src/jackhmmer@ --incE 0.01 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--incT @src/jackhmmer@ --incT 20 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--incdomE @src/jackhmmer@ --incdomE 0.01 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--incdomT @src/jackhmmer@ --incdomT 20 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--max @src/jackhmmer@ --max --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--F1 @src/jackhmmer@ --F1 0.03 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--F2 @src/jackhmmer@ --F2 0.002 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--F3 @src/jackhmmer@ --F3 0.0002 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--nobias @src/jackhmmer@ --nobias --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% # builder options untested 1 exercise j/--EmL @src/jackhmmer@ --EmL 100 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--EmN @src/jackhmmer@ --EmN 250 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--EvL @src/jackhmmer@ --EvL 100 --EmL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--EvN @src/jackhmmer@ --EvN 250 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--EfL @src/jackhmmer@ --EfL 100 --EmL 10 --EvL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--EfN @src/jackhmmer@ --EfN 250 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--Eft @src/jackhmmer@ --Eft 0.045 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--nonull2 @src/jackhmmer@ --nonull2 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/-Z @src/jackhmmer@ -Z 45000000 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--domZ @src/jackhmmer@ --domZ 45000000 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--seed @src/jackhmmer@ --seed 42 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--qformat @src/jackhmmer@ --qformat fasta --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise j/--tformat @src/jackhmmer@ --tformat fasta --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% # --cpu: threads only # --mpi: MPI only 1 prep cleanup rm -f %JHMMER.ch%-1.hmm %JHMMER.ca%-1.sto # phmmer xxxxxxxxxxxxxxxxxxxx 1 exercise phmmer @src/phmmer@ --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/-h @src/phmmer@ -h 1 exercise phmmer/-o @src/phmmer@ -o %PHMMER.out% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/-A @src/phmmer@ -A %PHMMER.sto% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--tblout @src/phmmer@ --tblout %PHMMER.tbl% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--domtblout @src/phmmer@ --domtblout %PHMMER.dtbl% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--pfamtblout @src/phmmer@ --pfamtblout %PHMMER.dtbl% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--acc @src/phmmer@ --acc --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--noali @src/phmmer@ --noali --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--notextw @src/phmmer@ --notextw --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--textw @src/phmmer@ --textw 256 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--popen @src/phmmer@ --popen 0.4 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--pextend @src/phmmer@ --pextend 0.6 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--mxfile @src/phmmer@ --mxfile !easel/formats/BLOSUM62! --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/-E @src/phmmer@ -E 0.01 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/-T @src/phmmer@ -T 20 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--domE @src/phmmer@ --domE 0.01 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--domT @src/phmmer@ --domT 20 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--incE @src/phmmer@ --incE 0.01 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--incT @src/phmmer@ --incT 20 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--incdomE @src/phmmer@ --incdomE 0.01 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--incdomT @src/phmmer@ --incdomT 20 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--max @src/phmmer@ --max --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--F1 @src/phmmer@ --F1 0.03 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--F2 @src/phmmer@ --F2 0.002 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--F3 @src/phmmer@ --F3 0.0002 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--nobias @src/phmmer@ --nobias --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--EmL @src/phmmer@ --EmL 100 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--EmN @src/phmmer@ --EmN 250 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--EvL @src/phmmer@ --EvL 100 --EmL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--EvN @src/phmmer@ --EvN 250 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--EfL @src/phmmer@ --EfL 100 --EmL 10 --EvL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--EfN @src/phmmer@ --EfN 250 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--Eft @src/phmmer@ --Eft 0.045 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--nonull2 @src/phmmer@ --nonull2 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/-Z @src/phmmer@ -Z 45000000 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--domZ @src/phmmer@ --domZ 45000000 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--seed @src/phmmer@ --seed 42 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--qformat @src/phmmer@ --qformat fasta --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 1 exercise phmmer/--tformat @src/phmmer@ --tformat fasta --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% # --cpu: threads only # --mpi: MPI only # nhmmer xxxxxxxxxxxxxxxxxxxx 1 prep rnddb @easel/miniapps/esl-shuffle@ -G --dna -L 10000 -N 2 -o %RNDDB% 1 exercise nhmmer @src/nhmmer@ !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/-h @src/nhmmer@ -h 1 exercise nhmmer/-o @src/nhmmer@ -o %nhmmer.out% !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/-A @src/nhmmer@ -A %nhmmer.sto% !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/--tblout @src/nhmmer@ --tblout %nhmmer.tbl% !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/--dfamtblout @src/nhmmer@ --dfamtblout %nhmmer.dtbl% !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/--acc @src/nhmmer@ --acc !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/--noali @src/nhmmer@ --noali !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/--notextw @src/nhmmer@ --notextw !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/--textw @src/nhmmer@ --textw 256 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/-E @src/nhmmer@ -E 0.01 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/-T @src/nhmmer@ -T 20 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/--incE @src/nhmmer@ --incE 0.01 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/--incT @src/nhmmer@ --incT 20 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/--max @src/nhmmer@ --max !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/--F1 @src/nhmmer@ --F1 0.03 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/--F2 @src/nhmmer@ --F2 0.002 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/--F3 @src/nhmmer@ --F3 0.0002 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/--nobias @src/nhmmer@ --nobias !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/--nonull2 @src/nhmmer@ --nonull2 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/-Z @src/nhmmer@ -Z 45000000 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmer/--seed @src/nhmmer@ --seed 42 !tutorial/MADE1.hmm! %RNDDB% # nhmmscan xxxxxxxxxxxxxxxxxxxx 1 prep rnddb @easel/miniapps/esl-shuffle@ -G --dna -L 10000 -N 2 -o %RNDDB% 1 prep press @src/hmmpress@ -f !tutorial/MADE1.hmm! 1 exercise nhmmscan @src/nhmmscan@ !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/-h @src/nhmmscan@ -h 1 exercise nhmmscan/-o @src/nhmmscan@ -o %nhmmscan.out% !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/--tblout @src/nhmmscan@ --tblout %nhmmscan.tbl% !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/--dfamtblout @src/nhmmscan@ --dfamtblout %nhmmscan.dtbl% !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/--acc @src/nhmmscan@ --acc !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/--noali @src/nhmmscan@ --noali !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/--notextw @src/nhmmscan@ --notextw !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/--textw @src/nhmmscan@ --textw 256 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/-E @src/nhmmscan@ -E 0.01 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/-T @src/nhmmscan@ -T 20 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/--incE @src/nhmmscan@ --incE 0.01 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/--incT @src/nhmmscan@ --incT 20 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/--max @src/nhmmscan@ --max !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/--F1 @src/nhmmscan@ --F1 0.03 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/--F2 @src/nhmmscan@ --F2 0.002 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/--F3 @src/nhmmscan@ --F3 0.0002 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/--nobias @src/nhmmscan@ --nobias !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/--nonull2 @src/nhmmscan@ --nonull2 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/-Z @src/nhmmscan@ -Z 45000000 !tutorial/MADE1.hmm! %RNDDB% 1 exercise nhmmscan/--seed @src/nhmmscan@ --seed 42 !tutorial/MADE1.hmm! %RNDDB% 1 prep cleanup rm !tutorial/MADE1.hmm!.h3? # hmmemit xxxxxxxxxxxxxxxxxxxx 1 exercise hmmemit @src/hmmemit@ !testsuite/Caudal_act.hmm! 1 exercise hmmemit/-h @src/hmmemit@ -h 1 exercise hmmemit/-c @src/hmmemit@ -c !testsuite/Caudal_act.hmm! 1 exercise hmmemit/-o @src/hmmemit@ -o /dev/null !testsuite/Caudal_act.hmm! 1 exercise hmmemit/-p @src/hmmemit@ -p !testsuite/Caudal_act.hmm! 1 exercise hmmemit/-N @src/hmmemit@ -N 10 !testsuite/Caudal_act.hmm! 1 exercise hmmemit/-L @src/hmmemit@ -p -L 50 !testsuite/Caudal_act.hmm! 1 exercise hmmemit/--local @src/hmmemit@ -p --local !testsuite/Caudal_act.hmm! 1 exercise hmmemit/--unilocal @src/hmmemit@ -p --unilocal !testsuite/Caudal_act.hmm! 1 exercise hmmemit/--glocal @src/hmmemit@ -p --glocal !testsuite/Caudal_act.hmm! 1 exercise hmmemit/--uniglocal @src/hmmemit@ -p --uniglocal !testsuite/Caudal_act.hmm! # xxxxxxxxx xxxxxxxxxxxxxxxxxxxx 1 exercise hmmfetch @src/hmmfetch@ %MINIFAM.HMM% Caudal_act 1 exercise hmmstat @src/hmmstat@ !testsuite/Caudal_act.hmm! 1 exercise hmmlogo @src/hmmlogo@ !testsuite/Caudal_act.hmm! 1 exercise hmmconvert @src/hmmconvert@ !testsuite/Caudal_act.hmm! 1 exercise hmmsim @src/hmmsim@ !testsuite/Caudal_act.hmm! ################################################################# # Integration tests ################################################################ # Run-to-run variation tests # By default, stochastic simulations are seeded reproducibly, so there # is no run-to-run variation; whereas with different RNG seeds, # run-to-run variation does occur. [xref J5/99] # The hmmemit seed of 35 is carefully chosen to generate a target sequence # that requires stochastic clustering when aligned to the Caudal_act.hmm test # To search for new seeds, the command line is something like: # ( ../src/hmmemit --seed 35 -p Caudal_act.hmm | ../src/hmmsearch --seed 2 --tblout foo.out Caudal_act.hmm - > /dev/null ; cat foo.out ) # looking for high scoring sequences that force a stochastic clustering step. # # xxxxxxxxxxxxxxxxxxxx 1 prep seq @src/hmmemit@ --seed 35 -p %CAUDAL.HMM% > %TESTSEQ% 1 prep db_1 @src/hmmemit@ --seed 35 -p %CAUDAL.HMM% > %TESTDB% 1 prep db_2 @easel/miniapps/esl-reformat@ fasta !testsuite/Caudal_act.sto! >> %TESTDB% 1 prep db_3 @easel/miniapps/esl-shuffle@ -G --amino -N 100 -L 350 >> %TESTDB% 1 exercise hmmbuild_variation !testsuite/i1-build-variation.sh! @src/hmmbuild@ !testsuite/Caudal_act.sto! %OUTFILES% 1 exercise hmmscan_variation !testsuite/i2-search-variation.sh! @src/hmmscan@ %MINIFAM.HMM% %TESTSEQ% %OUTFILES% 1 exercise hmmsearch_variation !testsuite/i2-search-variation.sh! @src/hmmsearch@ %CAUDAL.HMM% %TESTDB% %OUTFILES% 1 exercise phmmer_variation !testsuite/i3-seqsearch-variation.sh! @src/phmmer@ %OUTFILES% 3 exercise jackhmmer_variation !testsuite/i3-seqsearch-variation.sh! @src/jackhmmer@ %OUTFILES% 1 exercise mapali !testsuite/i6-hmmalign-mapali.pl! @src/hmmalign@ @easel/miniapps/esl-reformat@ !testsuite! %OUTFILES% 1 exercise fragments !testsuite/i7-hmmbuild-fragments.pl! @src/hmmbuild@ %OUTFILES% 1 exercise nonresidues !testsuite/i8-nonresidues.pl! @@ !! %OUTFILES% 1 exercise opt-annotation !testsuite/i9-optional-annotation.pl! @@ !! %OUTFILES% 1 exercise dup-names !testsuite/i10-duplicate-names.pl! @@ !! %OUTFILES% 1 exercise mapali-again !testsuite/i11-hmmalign-mapali.pl! @@ !! %OUTFILES% 1 exercise delete-corruption !testsuite/i12-delete-corruption.pl! @@ !! %OUTFILES% 1 exercise msa-integrity !testsuite/i13-msa-integrity.pl! @@ !! %OUTFILES% 1 exercise hmmemit-consensus !testsuite/i14-hmmemit-consensus.pl! @@ !! %OUTFILES% 1 exercise hmmconvert !testsuite/i15-hmmconvert.pl! @@ !! %OUTFILES% 1 exercise stdin_pipes !testsuite/i17-stdin.pl! @@ !! %OUTFILES% 1 exercise nhmmer_generic !testsuite/i18-nhmmer-generic.pl! @@ !! %OUTFILES% 1 exercise hmmpgmd_ga !testsuite/i19-hmmpgmd-ga.pl! @@ !! %OUTFILES% #comment out fmindex test until it's been returned to life #1 exercise fmindex-core !testsuite/i20-fmindex-core.pl! @@ !! %OUTFILES% 1 exercise rewind !testsuite/i21-rewind.pl! @@ !! %OUTFILES% 1 exercise hmmpgmd_shard_ga !testsuite/i22-hmmpgmd-shard-ga.pl! @@ !! %OUTFILES% 1 exercise bad-fasta !testsuite/i23-bad-fasta.sh! @@ !! %OUTFILES% 1 exercise brute-itest @src/itest_brute@ 1 exercise hmmpress-itest !src/hmmpress.itest.pl! @src/hmmpress@ %MINIFAM.HMM% %TMPPFX% ################################################################ # Fixed bug tests ################################################################ # xxxxxxxxxxxxxxxxxxxx 1 exercise h39 @src/hmmsearch@ !testsuite/M1.hmm! !testsuite/M1.sto! 1 exercise h45 !testsuite/i4-zerolength-seqs.sh! @@ !! %MINIFAM.HMM% %OUTFILES% 1 exercise h50 !testsuite/i5-hmmbuild-naming.pl! @@ !! %OUTFILES% 1 exercise h82 !testsuite/i16-build-allins.pl! @@ !! %OUTFILES% 1 exercise iss159 !testsuite/iss159-nhmmer-overlap.py! @@ !! %OUTFILES% ################################################################ # valgrind tests (optional. 'make SQCLEVEL=3 check') ################################################################ # xxxxxxxxxxxxxxxxxxxx 3 valgrind hmmer @src/hmmer_utest@ 3 valgrind build @src/build_utest@ 3 valgrind generic_fwdback @src/generic_fwdback_utest@ 3 valgrind generic_msv @src/generic_msv_utest@ 3 valgrind generic_stotrace @src/generic_stotrace_utest@ 3 valgrind generic_viterbi @src/generic_viterbi_utest@ 3 valgrind logsum @src/logsum_utest@ 3 valgrind modelconfig @src/modelconfig_utest@ 3 valgrind p7_alidisplay @src/p7_alidisplay_utest@ 3 valgrind p7_bg @src/p7_bg_utest@ 3 valgrind p7_gmx @src/p7_gmx_utest@ 3 valgrind p7_hmm @src/p7_hmm_utest@ 3 valgrind p7_hmmfile @src/p7_hmmfile_utest@ 3 valgrind p7_profile @src/p7_profile_utest@ 3 valgrind p7_tophits @src/p7_tophits_utest@ 3 valgrind p7_trace @src/p7_trace_utest@ 3 valgrind decoding @src/impl/decoding_utest@ 3 valgrind fwdback @src/impl/fwdback_utest@ 3 valgrind io @src/impl/io_utest@ 3 valgrind msvfilter @src/impl/msvfilter_utest@ 3 valgrind null2 @src/impl/null2_utest@ 3 valgrind optacc @src/impl/optacc_utest@ 3 valgrind stotrace @src/impl/stotrace_utest@ 3 valgrind vitfilter @src/impl/vitfilter_utest@ 1 prep minifam @src/hmmbuild@ %MINIFAM.HMM% !testsuite/minifam! 3 valgrind hmmbuild @src/hmmbuild@ %GLOBIN.HMM% !tutorial/globins4.sto! 3 valgrind hmmconvert @src/hmmconvert@ -b %GLOBIN.HMM% 3 valgrind hmmalign @src/hmmalign@ %GLOBIN.HMM% !tutorial/globins45.fa! 3 valgrind hmmemit @src/hmmemit@ -N10 %GLOBIN.HMM% 3 valgrind hmmpress @src/hmmpress@ -f %MINIFAM.HMM% 3 valgrind hmmfetch @src/hmmfetch@ %MINIFAM.HMM% Caudal_act 3 valgrind hmmscan @src/hmmscan@ %MINIFAM.HMM% !tutorial/HBB_HUMAN! 3 valgrind hmmsearch @src/hmmsearch@ %GLOBIN.HMM% !tutorial/globins45.fa! 3 valgrind hmmsim @src/hmmsim@ %GLOBIN.HMM% 3 valgrind hmmstat @src/hmmstat@ %MINIFAM.HMM% 3 valgrind jackhmmer @src/jackhmmer@ !tutorial/HBB_HUMAN! !tutorial/globins45.fa! 3 valgrind phmmer @src/phmmer@ !tutorial/HBB_HUMAN! !tutorial/globins45.fa! 3 valgrind nhmmer @src/nhmmer@ !tutorial/MADE1.hmm! !tutorial/dna_target.fa! # some derivatives of tmpfiles created by hmmpress, not sqc itself: clean up 1 prep minifam rm -f %MINIFAM.HMM%.h3f %MINIFAM.HMM%.h3p %MINIFAM.HMM%.h3m %MINIFAM.HMM%.h3i