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/tetraloop.dh ADDED Viewed

@@ -0,0 +1,77 @@
+AAAAAT	500
+AAAACT	700
+AAACAT	1000
+ACTTGT	0
+AGAAAT	-1100
+AGAGAT	-1100
+AGATAT	-1500
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+AGGGGT	500
+AGTAAT	-1600
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+AGTTCT	800
+ATTCGT	-200
+ATTTGT	0
+ATTTTT	-500
+CAAAAG	500
+CAAACG	700
+CAACAG	1000
+CAACCG	0
+CCTTGG	0
+CGAAAG	-1100
+CGAGAG	-1100
+CGATAG	-1500
+CGCAAG	-1600
+CGCGAG	-1100
+CGCTTG	200
+CGGAAG	-1100
+CGGGAG	-1000
+CGGGGG	500
+CGTAAG	-1600
+CGTGAG	-1100
+CGTTCG	800
+CTTCGG	-200
+CTTTGG	0
+CTTTTG	-500
+GAAAAC	500
+GAAACC	700
+GAACAC	1000
+GCTTGC	0
+GGAAAC	-1100
+GGAGAC	-1100
+GGATAC	-1600
+GGCAAC	-1600
+GGCGAC	-1100
+GGCTTC	200
+GGGAAC	-1100
+GGGGAC	-1100
+GGGGGC	500
+GGTAAC	-1600
+GGTGAC	-1100
+GGTTCC	800
+GTTCGC	-200
+GTTTGC	0
+GTTTTC	-500
+TAAAAA	500
+TAAACA	700
+TAACAA	1000
+TCTTGA	0
+TGAAAA	-1100
+TGAGAA	-1100
+TGATAA	-1600
+TGCAAA	-1600
+TGCGAA	-1100
+TGCTTA	200
+TGGAAA	-1100
+TGGGAA	-1100
+TGGGGA	500
+TGTAAA	-1600
+TGTGAA	-1100
+TGTTCA	800
+TTTCGA	-200
+TTTTGA	0
+TTTTTA	-500

data/lib/qu/cmdwrapper/primer3_config/tetraloop.ds ADDED Viewed

@@ -0,0 +1,77 @@
+AAAAAT	-650
+AAAACT	1610
+AAACAT	1610
+ACTTGT	4190
+AGAAAT	1610
+AGAGAT	1610
+AGATAT	1610
+AGCAAT	1610
+AGCGAT	1610
+AGCTTT	1610
+AGGAAT	1610
+AGGGAT	1610
+AGGGGT	640
+AGTAAT	1610
+AGTGAT	1610
+AGTTCT	1610
+ATTCGT	1610
+ATTTGT	1610
+ATTTTT	1610
+CAAAAG	-1290
+CAAACG	0
+CAACAG	0
+CAACCG	0
+CCTTGG	2570
+CGAAAG	0
+CGAGAG	0
+CGATAG	0
+CGCAAG	0
+CGCGAG	0
+CGCTTG	0
+CGGAAG	0
+CGGGAG	0
+CGGGGG	-970
+CGTAAG	0
+CGTGAG	0
+CGTTCG	0
+CTTCGG	0
+CTTTGG	0
+CTTTTG	0
+GAAAAC	-3230
+GAAACC	0
+GAACAC	0
+GCTTGC	2570
+GGAAAC	0
+GGAGAC	0
+GGATAC	0
+GGCAAC	0
+GGCGAC	0
+GGCTTC	0
+GGGAAC	0
+GGGGAC	0
+GGGGGC	-970
+GGTAAC	0
+GGTGAC	0
+GGTTCC	0
+GTTCGC	0
+GTTTGC	0
+GTTTTC	0
+TAAAAA	320
+TAAACA	1610
+TAACAA	1610
+TCTTGA	4190
+TGAAAA	1610
+TGAGAA	1610
+TGATAA	1610
+TGCAAA	1610
+TGCGAA	1610
+TGCTTA	1610
+TGGAAA	1610
+TGGGAA	1610
+TGGGGA	640
+TGTAAA	1610
+TGTGAA	1610
+TGTTCA	1610
+TTTCGA	1610
+TTTTGA	1610
+TTTTTA	1610

data/lib/qu/cmdwrapper/primer3_config/triloop.dh ADDED Viewed

@@ -0,0 +1,16 @@
+AGAAT	-1500
+AGCAT	-1500
+AGGAT	-1500
+AGTAT	-1500
+CGAAG	-2000
+CGCAG	-2000
+CGGAG	-2000
+CGTAG	-2000
+GGAAC	-2000
+GGCAC	-2000
+GGGAC	-2000
+GGTAC	-2000
+TGAAA	-1500
+TGCAA	-1500
+TGGAA	-1500
+TGTAA	-1500

data/lib/qu/cmdwrapper/primer3_config/triloop.ds ADDED Viewed

@@ -0,0 +1,16 @@
+AGAAT	0
+AGCAT	0
+AGGAT	0
+AGTAT	0
+CGAAG	0
+CGCAG	0
+CGGAG	0
+CGTAG	0
+GGAAC	0
+GGCAC	0
+GGGAC	0
+GGTAC	0
+TGAAA	0
+TGCAA	0
+TGGAA	0
+TGTAA	0

data/lib/qu/cmdwrapper/primer3_config/tstack.dh ADDED Viewed

@@ -0,0 +1,256 @@
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data/lib/qu/cmdwrapper/primer3_config/tstack2.dh ADDED Viewed

@@ -0,0 +1,256 @@
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