RubyGems - qu-cmdwrapper - Versions diffs - 1.0.0 - Mend

qu-cmdwrapper 1.0.0

Files changed (67) hide show

checksums.yaml +7 -0
data/.gitignore +17 -0
data/Gemfile +5 -0
data/LICENSE.txt +22 -0
data/README.md +32 -0
data/Rakefile +1 -0
data/lib/qu/cmdwrapper.rb +10 -0
data/lib/qu/cmdwrapper/cmd.rb +109 -0
data/lib/qu/cmdwrapper/ext_bin/linux/32/faToTwoBit +0 -0
data/lib/qu/cmdwrapper/ext_bin/linux/32/ntdpal +0 -0
data/lib/qu/cmdwrapper/ext_bin/linux/32/ntthal +0 -0
data/lib/qu/cmdwrapper/ext_bin/linux/32/oligotm +0 -0
data/lib/qu/cmdwrapper/ext_bin/linux/32/primer3_core +0 -0
data/lib/qu/cmdwrapper/ext_bin/linux/32/twoBitToFa +0 -0
data/lib/qu/cmdwrapper/ext_bin/linux/64/faToTwoBit +0 -0
data/lib/qu/cmdwrapper/ext_bin/linux/64/ntdpal +0 -0
data/lib/qu/cmdwrapper/ext_bin/linux/64/ntthal +0 -0
data/lib/qu/cmdwrapper/ext_bin/linux/64/oligotm +0 -0
data/lib/qu/cmdwrapper/ext_bin/linux/64/primer3_core +0 -0
data/lib/qu/cmdwrapper/ext_bin/linux/64/twoBitToFa +0 -0
data/lib/qu/cmdwrapper/ext_bin/mac/32/faToTwoBit +0 -0
data/lib/qu/cmdwrapper/ext_bin/mac/32/ntthal +0 -0
data/lib/qu/cmdwrapper/ext_bin/mac/32/oligotm +0 -0
data/lib/qu/cmdwrapper/ext_bin/mac/32/primer3_core +0 -0
data/lib/qu/cmdwrapper/ext_bin/mac/32/twoBitToFa +0 -0
data/lib/qu/cmdwrapper/ext_bin/mac/64/faToTwoBit +0 -0
data/lib/qu/cmdwrapper/ext_bin/mac/64/ntthal +0 -0
data/lib/qu/cmdwrapper/ext_bin/mac/64/oligotm +0 -0
data/lib/qu/cmdwrapper/ext_bin/mac/64/primer3_core +0 -0
data/lib/qu/cmdwrapper/ext_bin/mac/64/twoBitToFa +0 -0
data/lib/qu/cmdwrapper/primer3_config/dangle.dh +128 -0
data/lib/qu/cmdwrapper/primer3_config/dangle.ds +128 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/dangle_i.dh +131 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/dangle_i.ds +131 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/loops_i.dh +34 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/loops_i.ds +31 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/stack_i.dh +257 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/stack_i.ds +256 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/stackmm_i_mm.dh +257 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/stackmm_i_mm.ds +256 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/tetraloop_i.dh +79 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/tetraloop_i.ds +81 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/triloop_i.dh +21 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/triloop_i.ds +18 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack2_i.dh +256 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack2_i.ds +256 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_i.dh +256 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_i.ds +256 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_tm_inf_i.dh +256 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_tm_inf_i.ds +256 -0
data/lib/qu/cmdwrapper/primer3_config/loops.dh +30 -0
data/lib/qu/cmdwrapper/primer3_config/loops.ds +30 -0
data/lib/qu/cmdwrapper/primer3_config/stack.dh +256 -0
data/lib/qu/cmdwrapper/primer3_config/stack.ds +256 -0
data/lib/qu/cmdwrapper/primer3_config/stackmm.dh +256 -0
data/lib/qu/cmdwrapper/primer3_config/stackmm.ds +256 -0
data/lib/qu/cmdwrapper/primer3_config/tetraloop.dh +77 -0
data/lib/qu/cmdwrapper/primer3_config/tetraloop.ds +77 -0
data/lib/qu/cmdwrapper/primer3_config/triloop.dh +16 -0
data/lib/qu/cmdwrapper/primer3_config/triloop.ds +16 -0
data/lib/qu/cmdwrapper/primer3_config/tstack.dh +256 -0
data/lib/qu/cmdwrapper/primer3_config/tstack2.dh +256 -0
data/lib/qu/cmdwrapper/primer3_config/tstack2.ds +256 -0
data/lib/qu/cmdwrapper/primer3_config/tstack_tm_inf.ds +256 -0
data/lib/qu/cmdwrapper/version.rb +5 -0
data/qu-cmdwrapper.gemspec +24 -0
metadata +137 -0

data/lib/qu/cmdwrapper/primer3_config/interpretations/stack_i.ds ADDED Viewed

@@ -0,0 +1,256 @@
+AA_AA	inf
+AA_AC	inf
+AA_AG	inf
+AA_AT	inf
+AA_CA	inf
+AA_CC	inf
+AA_CG	inf
+AA_CT	inf
+AA_GA	inf
+AA_GC	inf
+AA_GG	inf
+AA_GT	inf
+AA_TA	inf
+AA_TC	inf
+AA_TG	inf
+AA_TT	-22.2
+AC_AA	inf
+AC_AC	inf
+AC_AG	inf
+AC_AT	inf
+AC_CA	inf
+AC_CC	inf
+AC_CG	inf
+AC_CT	inf
+AC_GA	inf
+AC_GC	inf
+AC_GG	inf
+AC_GT	inf
+AC_TA	inf
+AC_TC	inf
+AC_TG	-22.4
+AC_TT	inf
+AG_AA	inf
+AG_AC	inf
+AG_AG	inf
+AG_AT	inf
+AG_CA	inf
+AG_CC	inf
+AG_CG	inf
+AG_CT	inf
+AG_GA	inf
+AG_GC	-13.2
+AG_GG	inf
+AG_GT	inf
+AG_TA	inf
+AG_TC	-21.0
+AG_TG	inf
+AG_TT	inf
+AT_AA	inf
+AT_AC	inf
+AT_AG	inf
+AT_AT	inf
+AT_CA	inf
+AT_CC	inf
+AT_CG	inf
+AT_CT	inf
+AT_GA	inf
+AT_GC	inf
+AT_GG	inf
+AT_GT	inf
+AT_TA	-20.4
+AT_TC	inf
+AT_TG	inf
+AT_TT	inf
+CA_AA	inf
+CA_AC	inf
+CA_AG	inf
+CA_AT	inf
+CA_CA	inf
+CA_CC	inf
+CA_CG	inf
+CA_CT	inf
+CA_GA	inf
+CA_GC	inf
+CA_GG	inf
+CA_GT	-22.7
+CA_TA	inf
+CA_TC	inf
+CA_TG	inf
+CA_TT	inf
+CC_AA	inf
+CC_AC	inf
+CC_AG	inf
+CC_AT	inf
+CC_CA	inf
+CC_CC	inf
+CC_CG	inf
+CC_CT	inf
+CC_GA	inf
+CC_GC	inf
+CC_GG	-19.9
+CC_GT	inf
+CC_TA	inf
+CC_TC	inf
+CC_TG	inf
+CC_TT	inf
+CG_AA	inf
+CG_AC	inf
+CG_AG	inf
+CG_AT	inf
+CG_CA	inf
+CG_CC	inf
+CG_CG	inf
+CG_CT	inf
+CG_GA	inf
+CG_GC	-27.2
+CG_GG	inf
+CG_GT	inf
+CG_TA	inf
+CG_TC	inf
+CG_TG	inf
+CG_TT	inf
+CT_AA	inf
+CT_AC	inf
+CT_AG	inf
+CT_AT	inf
+CT_CA	inf
+CT_CC	inf
+CT_CG	inf
+CT_CT	inf
+CT_GA	-21.0
+CT_GC	inf
+CT_GG	inf
+CT_GT	-15.8
+CT_TA	inf
+CT_TC	inf
+CT_TG	inf
+CT_TT	inf
+GA_AA	inf
+GA_AC	inf
+GA_AG	inf
+GA_AT	inf
+GA_CA	inf
+GA_CC	inf
+GA_CG	inf
+GA_CT	-22.2
+GA_GA	inf
+GA_GC	inf
+GA_GG	inf
+GA_GT	inf
+GA_TA	inf
+GA_TC	inf
+GA_TG	inf
+GA_TT	inf
+GC_AA	inf
+GC_AC	inf
+GC_AG	inf
+GC_AT	inf
+GC_CA	inf
+GC_CC	inf
+GC_CG	-24.4
+GC_CT	inf
+GC_GA	inf
+GC_GC	inf
+GC_GG	inf
+GC_GT	inf
+GC_TA	inf
+GC_TC	inf
+GC_TG	inf
+GC_TT	inf
+GG_AA	inf
+GG_AC	inf
+GG_AG	inf
+GG_AT	inf
+GG_CA	inf
+GG_CC	-19.9
+GG_CG	-15.8
+GG_CT	inf
+GG_GA	inf
+GG_GC	inf
+GG_GG	inf
+GG_GT	inf
+GG_TA	inf
+GG_TC	inf
+GG_TG	inf
+GG_TT	inf
+GT_AA	inf
+GT_AC	inf
+GT_AG	inf
+GT_AT	inf
+GT_CA	-22.4
+GT_CC	inf
+GT_CG	inf
+GT_CT	inf
+GT_GA	inf
+GT_GC	inf
+GT_GG	inf
+GT_GT	inf
+GT_TA	inf
+GT_TC	inf
+GT_TG	inf
+GT_TT	inf
+TA_AA	inf
+TA_AC	inf
+TA_AG	inf
+TA_AT	-21.3
+TA_CA	inf
+TA_CC	inf
+TA_CG	inf
+TA_CT	inf
+TA_GA	inf
+TA_GC	inf
+TA_GG	inf
+TA_GT	inf
+TA_TA	inf
+TA_TC	inf
+TA_TG	inf
+TA_TT	inf
+TC_AA	inf
+TC_AC	inf
+TC_AG	-22.2
+TC_AT	inf
+TC_CA	inf
+TC_CC	inf
+TC_CG	inf
+TC_CT	inf
+TC_GA	inf
+TC_GC	inf
+TC_GG	inf
+TC_GT	inf
+TC_TA	inf
+TC_TC	inf
+TC_TG	inf
+TC_TT	inf
+TG_AA	inf
+TG_AC	-22.7
+TG_AG	inf
+TG_AT	inf
+TG_CA	inf
+TG_CC	inf
+TG_CG	inf
+TG_CT	inf
+TG_GA	inf
+TG_GC	inf
+TG_GG	inf
+TG_GT	inf
+TG_TA	inf
+TG_TC	inf
+TG_TG	inf
+TG_TT	inf
+TT_AA	-22.2
+TT_AC	inf
+TT_AG	inf
+TT_AT	inf
+TT_CA	inf
+TT_CC	inf
+TT_CG	inf
+TT_CT	inf
+TT_GA	-9
+TT_GC	inf
+TT_GG	inf
+TT_GT	inf
+TT_TA	inf
+TT_TC	inf
+TT_TG	inf
+TT_TT	inf

data/lib/qu/cmdwrapper/primer3_config/interpretations/stackmm_i_mm.dh ADDED Viewed

@@ -0,0 +1,257 @@
+/* values in articles are modified as follows: dS *(-10) and dH *(-10) */
+AA_AA inf
+AA_AC inf
+AA_AG inf
+AA_AT inf
+AA_CA inf
+AA_CC inf
+AA_CG inf
+AA_CT 7600
+AA_GA inf
+AA_GC inf
+AA_GG inf
+AA_GT 3000
+AA_TA 1200
+AA_TC 2300
+AA_TG -600
+AA_TT inf
+AC_AA inf
+AC_AC inf
+AC_AG -2900
+AC_AT inf
+AC_CA inf
+AC_CC inf
+AC_CG -700
+AC_CT inf
+AC_GA inf
+AC_GC inf
+AC_GG 500
+AC_GT inf
+AC_TA 5300
+AC_TC 0
+AC_TG  -8400
+AC_TT 700
+AG_AA inf
+AG_AC -900
+AG_AG inf
+AG_AT inf
+AG_CA inf
+AG_CC 600
+AG_CG inf
+AG_CT inf
+AG_GA inf
+AG_GC -4000
+AG_GG inf
+AG_GT inf
+AG_TA -700
+AG_TC inf
+AG_TG -3100
+AG_TT -1000
+AT_AA 1200
+AT_AC inf
+AT_AG inf
+AT_AT inf
+AT_CA 5300
+AT_CC inf
+AT_CG inf
+AT_CT inf
+AT_GA -700
+AT_GC inf
+AT_GG inf
+AT_GT inf
+AT_TA  -7200
+AT_TC -1200
+AT_TG -2500
+AT_TT -2700
+CA_AA inf
+CA_AC inf
+CA_AG inf
+CA_AT 3400
+CA_CA inf
+CA_CC inf
+CA_CG inf
+CA_CT 6100
+CA_GA -900
+CA_GC 1900
+CA_GG -700
+CA_GT inf
+CA_TA inf
+CA_TC inf
+CA_TG inf
+CA_TT 1000
+CC_AA inf
+CC_AC inf
+CC_AG 5200
+CC_AT inf
+CC_CA inf
+CC_CC inf
+CC_CG 3600
+CC_CT inf
+CC_GA 600
+CC_GC -1500
+CC_GG inf
+CC_GT -800
+CC_TA inf
+CC_TC inf
+CC_TG 5200
+CC_TT inf
+CG_AA inf
+CG_AC 1900
+CG_AG inf
+CG_AT inf
+CG_CA inf
+CG_CC -1500
+CG_CG inf
+CG_CT inf
+CG_GA -4000
+CG_GC inf
+CG_GG -4900
+CG_GT -4100
+CG_TA inf
+CG_TC -1500
+CG_TG inf
+CG_TT inf
+CT_AA 2300
+CT_AC inf
+CT_AG inf
+CT_AT inf
+CT_CA 0
+CT_CC inf
+CT_CG inf
+CT_CT inf
+CT_GA inf
+CT_GC -1500
+CT_GG -2800
+CT_GT -5000
+CT_TA -1200
+CT_TC inf
+CT_TG inf
+CT_TT inf
+GA_AA inf
+GA_AC inf
+GA_AG inf
+GA_AT 700
+GA_CA -2900
+GA_CC 5200
+GA_CG -600
+GA_CT inf
+GA_GA inf
+GA_GC inf
+GA_GG inf
+GA_GT 1600
+GA_TA inf
+GA_TC inf
+GA_TG inf
+GA_TT -1300
+GC_AA inf
+GC_AC inf
+GC_AG -600
+GC_AT inf
+GC_CA -700
+GC_CC 3600
+GC_CG inf
+GC_CT 2300
+GC_GA inf
+GC_GC inf
+GC_GG -6000
+GC_GT inf
+GC_TA inf
+GC_TC inf
+GC_TG -4400
+GC_TT inf
+GG_AA inf
+GG_AC -700
+GG_AG inf
+GG_AT inf
+GG_CA 500
+GG_CC inf
+GG_CG -6000
+GG_CT 3300
+GG_GA inf
+GG_GC -4900
+GG_GG inf
+GG_GT inf
+GG_TA inf
+GG_TC -2800
+GG_TG inf
+GG_TT 5800
+GT_AA -600
+GT_AC inf
+GT_AG inf
+GT_AT inf
+GT_CA inf
+GT_CC 5200
+GT_CG -4400
+GT_CT -2200
+GT_GA -3100
+GT_GC inf
+GT_GG inf
+GT_GT inf
+GT_TA -2500
+GT_TC inf
+GT_TG 4100
+GT_TT inf
+TA_AA 4700
+TA_AC 3400
+TA_AG 700
+TA_AT inf
+TA_CA inf
+TA_CC inf
+TA_CG inf
+TA_CT 1200
+TA_GA inf
+TA_GC inf
+TA_GG inf
+TA_GT -100
+TA_TA inf
+TA_TC inf
+TA_TG inf
+TA_TT 200
+TC_AA 7600
+TC_AC 6100
+TC_AG inf
+TC_AT 1200
+TC_CA inf
+TC_CC inf
+TC_CG 2300
+TC_CT inf
+TC_GA inf
+TC_GC inf
+TC_GG 3300
+TC_GT inf
+TC_TA inf
+TC_TC inf
+TC_TG -2200
+TC_TT inf
+TG_AA 3000
+TG_AC inf
+TG_AG 1600
+TG_AT -100
+TG_CA inf
+TG_CC -800
+TG_CG inf
+TG_CT inf
+TG_GA inf
+TG_GC -4100
+TG_GG inf
+TG_GT -1400
+TG_TA inf
+TG_TC -5000
+TG_TG inf
+TG_TT inf
+TT_AA inf
+TT_AC 1000
+TT_AG -1300
+TT_AT 200
+TT_CA 700
+TT_CC inf
+TT_CG inf
+TT_CT inf
+TT_GA -100
+TT_GC inf
+TT_GG 5800
+TT_GT inf
+TT_TA -2700
+TT_TC inf
+TT_TG inf
+TT_TT inf