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

qu-cmdwrapper 1.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

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/tstack2_i.dh ADDED Viewed

@@ -0,0 +1,256 @@
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+GC_AA 0
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+GC_CG -7000
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+GC_TG -5900
+GC_TT 0
+GG_AA 0
+GG_AC -3900
+GG_AG 0
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+GG_CA -4600
+GG_CC -7000
+GG_CG -700
+GG_CT -5700
+GG_GA 0
+GG_GC -3800
+GG_GG 0
+GG_GT 0
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+GG_TC -6600
+GG_TG 0
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+GT_AA -1900
+GT_AC 0
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+GT_CA -6000
+GT_CC -3000
+GT_CG -5900
+GT_CT -7400
+GT_GA -1100
+GT_GC 0
+GT_GG 0
+GT_GT 0
+GT_TA -3500
+GT_TC 0
+GT_TG 0
+GT_TT 0
+TA_AA -2500
+TA_AC -2300
+TA_AG -2000
+TA_AT -5000
+TA_CA 0
+TA_CC 0
+TA_CG 0
+TA_CT -2500
+TA_GA 0
+TA_GC 0
+TA_GG 0
+TA_GT -3900
+TA_TA 0
+TA_TC 0
+TA_TG 0
+TA_TT -3200
+TC_AA -2700
+TC_AC -700
+TC_AG -6000
+TC_AT -2500
+TC_CA 0
+TC_CC 0
+TC_CG -4900
+TC_CT 0
+TC_GA 0
+TC_GC 0
+TC_GG -5700
+TC_GT 0
+TC_TA 0
+TC_TC 0
+TC_TG -7400
+TC_TT 0
+TG_AA -2400
+TG_AC -6000
+TG_AG -1100
+TG_AT -3900
+TG_CA 0
+TG_CC -3200
+TG_CG 0
+TG_CT 0
+TG_GA 0
+TG_GC -3800
+TG_GG 0
+TG_GT 0
+TG_TA 0
+TG_TC -6100
+TG_TG 0
+TG_TT 0
+TT_AA -5000
+TT_AC -700
+TT_AG -3600
+TT_AT -3200
+TT_CA -900
+TT_CC 0
+TT_CG 0
+TT_CT 0
+TT_GA -3200
+TT_GC 0
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+TT_GT 0
+TT_TA -2400
+TT_TC 0
+TT_TG 0
+TT_TT 0

data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack2_i.ds ADDED Viewed

@@ -0,0 +1,256 @@
+AA_AA inf
+AA_AC inf
+AA_AG inf
+AA_AT -6.3
+AA_CA inf
+AA_CC inf
+AA_CG inf
+AA_CT -7.0
+AA_GA inf
+AA_GC inf
+AA_GG inf
+AA_GT -5.8
+AA_TA -7.8
+AA_TC -4.0
+AA_TG -4.4
+AA_TT -13.2
+AC_AA inf
+AC_AC inf
+AC_AG -22.5
+AC_AT inf
+AC_CA inf
+AC_CC inf
+AC_CG -7.1
+AC_CT inf
+AC_GA inf
+AC_GC inf
+AC_GG -11.4
+AC_GT inf
+AC_TA -3.8
+AC_TC -0.5
+AC_TG -16.1
+AC_TT -1.7
+AG_AA inf
+AG_AC -10.7
+AG_AG inf
+AG_AT inf
+AG_CA inf
+AG_CC -6.0
+AG_CG inf
+AG_CT inf
+AG_GA inf
+AG_GC -15.5
+AG_GG inf
+AG_GT inf
+AG_TA -5.9
+AG_TC -16.1
+AG_TG -2.1
+AG_TT -8.7
+AT_AA -7.8
+AT_AC inf
+AT_AG inf
+AT_AT inf
+AT_CA -3.8
+AT_CC inf
+AT_CG inf
+AT_CT inf
+AT_GA -5.9
+AT_GC inf
+AT_GG inf
+AT_GT inf
+AT_TA -13.6
+AT_TC -6.3
+AT_TG -9.4
+AT_TT -6.5
+CA_AA inf
+CA_AC inf
+CA_AG inf
+CA_AT -5.9
+CA_CA inf
+CA_CC inf
+CA_CG inf
+CA_CT -1.3
+CA_GA -10.7
+CA_GC -5.9
+CA_GG -9.6
+CA_GT -16.1
+CA_TA inf
+CA_TC inf
+CA_TG inf
+CA_TT -1.2
+CC_AA inf
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+CC_AG -13.8
+CC_AT inf
+CC_CA inf
+CC_CC inf
+CC_CG -10.6
+CC_CT inf
+CC_GA -6.0
+CC_GC -5.1
+CC_GG -19.3
+CC_GT -8.0
+CC_TA inf
+CC_TC inf
+CC_TG -7.8
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+CG_AA inf
+CG_AC -5.9
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+CG_GA -15.5
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+CG_GG -9.5
+CG_GT -9.0
+CG_TA inf
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+CG_TG inf
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+CT_AA -4.0
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+CT_GA -16.1
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+CT_GT -16.9
+CT_TA -6.3
+CT_TC inf
+CT_TG inf
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+GA_AA inf
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+GA_AT -4.7
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+GC_GG -19.2
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+GG_CT -15.9
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+GT_AA -4.4
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+TT_AA -13.5
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+TT_TA -6.5
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