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/tetraloop.dh ADDED Viewed

@@ -0,0 +1,77 @@
+AAAAAT	500
+AAAACT	700
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+GGTTCC	800
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+TGGGGA	500
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+TGTTCA	800
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+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
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+AGGGGT	640
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+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
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+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

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data/lib/qu/cmdwrapper/primer3_config/tstack2.dh ADDED Viewed

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