# HMMER option exercises, in sqc command format
# SRE, Thu Apr  3 08:23:27 2003
# CVS $Id: exercises.sqc,v 1.3 2003/10/03 19:12:59 eddy Exp $

# Option tests for hmm2align
#
1 prep        hmm2                  @hmm2build@ -F %OPT.HMM% Optiontests.slx
1 exercise    hmm2align             @hmm2align@ %OPT.HMM% Optiontests.fa
2 exercise    hmm2align/h           @hmm2align@ -h
2 exercise    hmm2align/m           @hmm2align@ -m %OPT.HMM% Optiontests.fa
2 exercise    hmm2align/o           @hmm2align@ -o %OPT.OUT% %OPT.HMM% Optiontests.fa
2 exercise    hmm2align/q           @hmm2align@ -q %OPT.HMM% Optiontests.fa
2 exercise    hmm2align/informat    @hmm2align@ --informat fasta %OPT.HMM% Optiontests.fa
2 exercise    hmm2align/selex       @hmm2align@ --outformat selex %OPT.HMM% Optiontests.fa
2 exercise    hmm2align/a2m         @hmm2align@ --outformat a2m %OPT.HMM% Optiontests.fa
2 exercise    hmm2align/clustal     @hmm2align@ --outformat clustal %OPT.HMM% Optiontests.fa
2 exercise    hmm2align/msf         @hmm2align@ --outformat msf %OPT.HMM% Optiontests.fa
2 exercise    hmm2align/phylip      @hmm2align@ --outformat phylip %OPT.HMM% Optiontests.fa
2 exercise    hmm2align/oneline     @hmm2align@ --oneline %OPT.HMM% Optiontests.fa
2 exercise    hmm2align/withali     @hmm2align@ --withali Optiontests.slx %OPT.HMM% Optiontests.fa
2 exercise    hmm2align/mapali      @hmm2align@ --mapali Optiontests.slx %OPT.HMM% Optiontests.fa

# Option tests for hmm2build.
#
1 exercise    hmm2build             @hmm2build@ %FN3.HMM% fn3.seed
2 exercise    hmm2build/h           @hmm2build@ -h
2 exercise    hmm2build/F           @hmm2build@ -F %FN3.HMM% Optiontests.nslx
2 exercise    hmm2build/n           @hmm2build@ -F -n foo %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/o           @hmm2build@ -F -o %OPT.OUT% %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/A           @hmm2build@ -F -A %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/f           @hmm2build@ -F -f %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/g           @hmm2build@ -F -g %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/s           @hmm2build@ -F -s %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/fast        @hmm2build@ -F --fast %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/hand        @hmm2build@ -F --hand %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/null        @hmm2build@ -F --null ./tutorial/nucleic.null %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/pam         @hmm2build@ -F --amino --pam Optiontests.pam %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/prior       @hmm2build@ -F --prior ./tutorial/nucleic.pri %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/wblosum     @hmm2build@ -F --wblosum %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/wgsc        @hmm2build@ -F --wgsc %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/wme         @hmm2build@ -F --wme %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/wpb         @hmm2build@ -F --wpb %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/wvoronoi    @hmm2build@ -F --wvoronoi %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/wnone       @hmm2build@ -F --wnone %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/noeff       @hmm2build@ -F --noeff %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/pbswitch    @hmm2build@ -F --pbswitch 4 %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/amino       @hmm2build@ -F --amino %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/nucleic     @hmm2build@ -F --nucleic %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/archpri     @hmm2build@ -F --archpri 0.5 %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/binary      @hmm2build@ -F --binary %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/cfile       @hmm2build@ -F --cfile %OPT.OUT% %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/gapmax      @hmm2build@ -F --gapmax 0.3 --fast %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/idlevel     @hmm2build@ -F --idlevel 0.8 %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/informat    @hmm2build@ -F --informat selex %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/pamwgt      @hmm2build@ -F --amino --pamwgt 50 --pam Optiontests.pam %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/swentry     @hmm2build@ -F --swentry 0.4 %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/swexit      @hmm2build@ -F --swexit 0.4 %OPT.HMM% Optiontests.nslx
2 exercise    hmm2build/verbose     @hmm2build@ -F --verbose %OPT.HMM% Optiontests.nslx

# Option tests for hmm2calibrate
#
1 prep        hmm2                  @hmm2build@ -F %OPT.HMM% Optiontests.nslx
1 exercise    hmm2calibrate         @hmm2calibrate@ %OPT.HMM%
2 exercise    hmm2calibrate/h       @hmm2calibrate@ -h
2 exercise    hmm2calibrate/fixed   @hmm2calibrate@ --fixed 15 %OPT.HMM%
2 exercise    hmm2calibrate/mean    @hmm2calibrate@ --mean  25 %OPT.HMM%
2 exercise    hmm2calibrate/hist    @hmm2calibrate@ --histfile %OPT.OUT% --fixed 15 %OPT.HMM%
2 exercise    hmm2calibrate/num     @hmm2calibrate@ --num 4500 --fixed 15 %OPT.HMM%
2 exercise    hmm2calibrate/sd      @hmm2calibrate@ --sd 50 --mean 25 %OPT.HMM%
2 exercise    hmm2calibrate/seed    @hmm2calibrate@ --seed 666 --fixed 15 %OPT.HMM%
  

# Option tests for hmm2convert
#
1 prep        hmm2                  @hmm2build@ -F --wnone --fast %OPT.HMM% fn3.seed
1 exercise    hmm2convert           @hmm2convert@ %OPT.HMM% %OPT.TMP%
2 exercise    hmm2convert/h         @hmm2convert@ -h
2 exercise    hmm2convert/F         @hmm2convert@ -F %OPT.HMM% %OPT.TMP%
2 exercise    hmm2convert/a         @hmm2convert@ -a -F %OPT.HMM% %OPT.TMP%
2 exercise    hmm2convert/A         @hmm2convert@ -A %OPT.HMM% %OPT.TMP%
2 exercise    hmm2convert/b         @hmm2convert@ -b -F %OPT.HMM% %OPT.TMP%
2 exercise    hmm2convert/p         @hmm2convert@ -p -F %OPT.HMM% %OPT.TMP%
2 exercise    hmm2convert/P         @hmm2convert@ -P -F %OPT.HMM% %OPT.TMP%

# Option tests for hmm2emit
#
1 prep        hmm2                  @hmm2build@ -F --wnone --fast %OPT.HMM% fn3.seed
1 exercise    hmm2emit              @hmm2emit@ %OPT.HMM%
2 exercise    hmm2emit/a            @hmm2emit@ -a %OPT.HMM%
2 exercise    hmm2emit/c            @hmm2emit@ -c %OPT.HMM%
2 exercise    hmm2emit/h            @hmm2emit@ -h
2 exercise    hmm2emit/n            @hmm2emit@ -n 6 %OPT.HMM%
2 exercise    hmm2emit/o            @hmm2emit@ -o %OPT.OUT% %OPT.HMM%
2 exercise    hmm2emit/q            @hmm2emit@ -q %OPT.HMM%
2 exercise    hmm2emit/seed         @hmm2emit@ --seed 666 %OPT.HMM%

# Option tests for hmm2index, hmm2fetch
#
1 prep        hmm2                  @hmm2build@ -n fn3 --wnone --fast -F %OPT.HMM% fn3.seed
1 prep        hmm2                  @hmm2build@ -n foo -A %OPT.HMM% Optiontests.slx
1 exercise    hmm2index             @hmm2index@ %OPT.HMM%
2 exercise    hmm2index/h           @hmm2index@ -h
1 exercise    hmm2fetch             @hmm2fetch@ %OPT.HMM% fn3
2 exercise    hmm2fetch/h           @hmm2fetch@ -h
2 exercise    hmm2fetch/n           @hmm2fetch@ -n %OPT.HMM% 1

# Option tests for hmm2pfam
#
1 prep        hmm2                  @hmm2build@ -F --nucleic %OPT.NHMM% Optiontests.nslx
1 prep        hmm2                  @hmm2build@ -F --amino %OPT.HMM% Optiontests.sto
1 exercise    hmm2pfam              @hmm2pfam@ %OPT.HMM% Optiontests.fa
2 exercise    hmm2pfam/h            @hmm2pfam@ -h
2 exercise    hmm2pfam/n            @hmm2pfam@ -n %OPT.NHMM% Optiontests.nfa
2 exercise    hmm2pfam/A            @hmm2pfam@ -A 0 %OPT.HMM% Optiontests.fa
2 exercise    hmm2pfam/E            @hmm2pfam@ -E 1 %OPT.HMM% Optiontests.fa
2 exercise    hmm2pfam/T            @hmm2pfam@ -T 1 %OPT.HMM% Optiontests.fa
2 exercise    hmm2pfam/Z            @hmm2pfam@ -Z 10 %OPT.HMM% Optiontests.fa
2 exercise    hmm2pfam/acc          @hmm2pfam@ --acc %OPT.HMM% Optiontests.fa
2 exercise    hmm2pfam/compat       @hmm2pfam@ --compat %OPT.HMM% Optiontests.fa
2 exercise    hmm2pfam/cut_ga       @hmm2pfam@ --cut_ga %OPT.HMM% Optiontests.fa
2 exercise    hmm2pfam/cut_nc       @hmm2pfam@ --cut_nc %OPT.HMM% Optiontests.fa
2 exercise    hmm2pfam/cut_tc       @hmm2pfam@ --cut_tc %OPT.HMM% Optiontests.fa
2 exercise    hmm2pfam/domE         @hmm2pfam@ --domE 1 %OPT.HMM% Optiontests.fa
2 exercise    hmm2pfam/domT         @hmm2pfam@ --domT 1 %OPT.HMM% Optiontests.fa
2 exercise    hmm2pfam/forward      @hmm2pfam@ --forward %OPT.HMM% Optiontests.fa
2 exercise    hmm2pfam/informat     @hmm2pfam@ --informat fasta %OPT.HMM% Optiontests.fa
2 exercise    hmm2pfam/null2        @hmm2pfam@ --null2 %OPT.HMM% Optiontests.fa
2 exercise    hmm2pfam/xnu          @hmm2pfam@ --xnu %OPT.HMM% Optiontests.fa

# Option tests for hmm2search
#
1 prep        hmm2                  @hmm2build@ -F --amino %OPT.HMM% Optiontests.sto
1 exercise    hmm2search            @hmm2search@ %OPT.HMM% Optiontests.fa
2 exercise    hmm2search/h          @hmm2search@ -h
2 exercise    hmm2search/A          @hmm2search@ -A 0 %OPT.HMM% Optiontests.fa
2 exercise    hmm2search/E          @hmm2search@ -E 1 %OPT.HMM% Optiontests.fa
2 exercise    hmm2search/T          @hmm2search@ -T 2 %OPT.HMM% Optiontests.fa
2 exercise    hmm2search/Z          @hmm2search@ -Z 10 %OPT.HMM% Optiontests.fa
2 exercise    hmm2search/compat     @hmm2search@ --compat %OPT.HMM% Optiontests.fa
2 exercise    hmm2search/cut_ga     @hmm2search@ --cut_ga %OPT.HMM% Optiontests.fa
2 exercise    hmm2search/cut_nc     @hmm2search@ --cut_nc %OPT.HMM% Optiontests.fa
2 exercise    hmm2search/cut_tc     @hmm2search@ --cut_tc %OPT.HMM% Optiontests.fa
2 exercise    hmm2search/domE       @hmm2search@ --domE 1.0 %OPT.HMM% Optiontests.fa
2 exercise    hmm2search/domT       @hmm2search@ --domT 1.0 %OPT.HMM% Optiontests.fa
2 exercise    hmm2search/forward    @hmm2search@ --forward  %OPT.HMM% Optiontests.fa
2 exercise    hmm2search/informat   @hmm2search@ --informat fasta %OPT.HMM% Optiontests.fa
2 exercise    hmm2search/null2      @hmm2search@ --null2  %OPT.HMM% Optiontests.fa
2 exercise    hmm2search/xnu        @hmm2search@ --xnu  %OPT.HMM% Optiontests.fa

# Compiled exercises
#
1 exercise    align_align         @alignalign_test@
1 exercise    evd                 @evd_test@
1 exercise    masks               @masks_test@
1 exercise    parsingv            @parsingviterbi_test@
1 exercise    tophits             @tophits_test@
1 exercise    trace               @trace_test@
1 exercise    viterbi             @viterbi_exercise@
1 exercise    weeviterbi          @weeviterbi_test@

# Test scripts
1 exercise    test1/conversion    ./test1-conversion.pl @hmm2convert@

