RubyGems - bio-polymarker - Versions diffs - 1.3.2 - Mend

bio-polymarker 1.3.2

Files changed (177) hide show

checksums.yaml +7 -0
data/.travis.yml +24 -0
data/Gemfile +23 -0
data/README.md +205 -0
data/Rakefile +61 -0
data/SECURITY.md +16 -0
data/VERSION +1 -0
data/bin/bfr.rb +128 -0
data/bin/blast_triads.rb +166 -0
data/bin/blast_triads_promoters.rb +192 -0
data/bin/count_variations.rb +36 -0
data/bin/filter_blat_by_target_coverage.rb +69 -0
data/bin/filter_exonerate_by_identity.rb +38 -0
data/bin/find_best_blat_hit.rb +33 -0
data/bin/find_best_exonerate.rb +17 -0
data/bin/get_longest_hsp_blastx_triads.rb +66 -0
data/bin/hexaploid_primers.rb +168 -0
data/bin/homokaryot_primers.rb +183 -0
data/bin/mafft_triads.rb +120 -0
data/bin/mafft_triads_promoters.rb +403 -0
data/bin/map_markers_to_contigs.rb +66 -0
data/bin/marker_to_vcf.rb +241 -0
data/bin/markers_in_region.rb +42 -0
data/bin/mask_triads.rb +169 -0
data/bin/polymarker.rb +410 -0
data/bin/polymarker_capillary.rb +443 -0
data/bin/polymarker_deletions.rb +350 -0
data/bin/snp_position_to_polymarker.rb +101 -0
data/bin/snps_between_bams.rb +107 -0
data/bin/tag_stats.rb +75 -0
data/bin/vcfLineToTable.rb +56 -0
data/bin/vcfToPolyMarker.rb +82 -0
data/bio-polymarker.gemspec +227 -0
data/conf/defaults.rb +1 -0
data/conf/primer3_config/dangle.dh +128 -0
data/conf/primer3_config/dangle.ds +128 -0
data/conf/primer3_config/interpretations/dangle_i.dh +131 -0
data/conf/primer3_config/interpretations/dangle_i.ds +131 -0
data/conf/primer3_config/interpretations/loops_i.dh +34 -0
data/conf/primer3_config/interpretations/loops_i.ds +31 -0
data/conf/primer3_config/interpretations/stack_i.dh +257 -0
data/conf/primer3_config/interpretations/stack_i.ds +256 -0
data/conf/primer3_config/interpretations/stackmm_i_mm.dh +257 -0
data/conf/primer3_config/interpretations/stackmm_i_mm.ds +256 -0
data/conf/primer3_config/interpretations/tetraloop_i.dh +79 -0
data/conf/primer3_config/interpretations/tetraloop_i.ds +81 -0
data/conf/primer3_config/interpretations/triloop_i.dh +21 -0
data/conf/primer3_config/interpretations/triloop_i.ds +18 -0
data/conf/primer3_config/interpretations/tstack2_i.dh +256 -0
data/conf/primer3_config/interpretations/tstack2_i.ds +256 -0
data/conf/primer3_config/interpretations/tstack_i.dh +256 -0
data/conf/primer3_config/interpretations/tstack_i.ds +256 -0
data/conf/primer3_config/interpretations/tstack_tm_inf_i.dh +256 -0
data/conf/primer3_config/interpretations/tstack_tm_inf_i.ds +256 -0
data/conf/primer3_config/loops.dh +30 -0
data/conf/primer3_config/loops.ds +30 -0
data/conf/primer3_config/stack.dh +256 -0
data/conf/primer3_config/stack.ds +256 -0
data/conf/primer3_config/stackmm.dh +256 -0
data/conf/primer3_config/stackmm.ds +256 -0
data/conf/primer3_config/tetraloop.dh +77 -0
data/conf/primer3_config/tetraloop.ds +77 -0
data/conf/primer3_config/triloop.dh +16 -0
data/conf/primer3_config/triloop.ds +16 -0
data/conf/primer3_config/tstack.dh +256 -0
data/conf/primer3_config/tstack2.dh +256 -0
data/conf/primer3_config/tstack2.ds +256 -0
data/conf/primer3_config/tstack_tm_inf.ds +256 -0
data/lib/bio/BFRTools.rb +465 -0
data/lib/bio/BIOExtensions.rb +153 -0
data/lib/bio/PolyploidTools/ChromosomeArm.rb +63 -0
data/lib/bio/PolyploidTools/ExonContainer.rb +245 -0
data/lib/bio/PolyploidTools/Marker.rb +175 -0
data/lib/bio/PolyploidTools/Mask.rb +116 -0
data/lib/bio/PolyploidTools/NoSNPSequence.rb +292 -0
data/lib/bio/PolyploidTools/PrimerRegion.rb +30 -0
data/lib/bio/PolyploidTools/SNP.rb +804 -0
data/lib/bio/PolyploidTools/SNPMutant.rb +86 -0
data/lib/bio/PolyploidTools/SNPSequence.rb +55 -0
data/lib/bio/db/blast.rb +114 -0
data/lib/bio/db/exonerate.rb +333 -0
data/lib/bio/db/primer3.rb +820 -0
data/lib/bio-polymarker.rb +28 -0
data/test/data/7B_amplicon_test.fa +12 -0
data/test/data/7B_amplicon_test.fa.fai +1 -0
data/test/data/7B_amplicon_test_reference.fa +110 -0
data/test/data/7B_amplicon_test_reference.fa.fai +3 -0
data/test/data/7B_marker_test.txt +1 -0
data/test/data/BS00068396_51.fa +2 -0
data/test/data/BS00068396_51_blast.tab +4 -0
data/test/data/BS00068396_51_contigs.aln +1412 -0
data/test/data/BS00068396_51_contigs.dnd +7 -0
data/test/data/BS00068396_51_contigs.fa +8 -0
data/test/data/BS00068396_51_contigs.fa.fai +4 -0
data/test/data/BS00068396_51_contigs.fa.nhr +0 -0
data/test/data/BS00068396_51_contigs.fa.nin +0 -0
data/test/data/BS00068396_51_contigs.fa.nsq +0 -0
data/test/data/BS00068396_51_contigs.nhr +0 -0
data/test/data/BS00068396_51_contigs.nin +0 -0
data/test/data/BS00068396_51_contigs.nsq +0 -0
data/test/data/BS00068396_51_exonerate.tab +6 -0
data/test/data/BS00068396_51_for_polymarker.txt +1 -0
data/test/data/BS00068396_51_genes.txt +14 -0
data/test/data/IWGSC_CSS_1AL_scaff_1455974.fa +112 -0
data/test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa +2304 -0
data/test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa.fai +11 -0
data/test/data/LIB1716.bam +0 -0
data/test/data/LIB1716.bam.bai +0 -0
data/test/data/LIB1719.bam +0 -0
data/test/data/LIB1719.bam.bai +0 -0
data/test/data/LIB1721.bam +0 -0
data/test/data/LIB1721.bam.bai +0 -0
data/test/data/LIB1722.bam +0 -0
data/test/data/LIB1722.bam.bai +0 -0
data/test/data/PST130_7067.csv +1 -0
data/test/data/PST130_7067.fa +2 -0
data/test/data/PST130_7067.fa.fai +1 -0
data/test/data/PST130_7067.fa.ndb +0 -0
data/test/data/PST130_7067.fa.nhr +0 -0
data/test/data/PST130_7067.fa.nin +0 -0
data/test/data/PST130_7067.fa.not +0 -0
data/test/data/PST130_7067.fa.nsq +0 -0
data/test/data/PST130_7067.fa.ntf +0 -0
data/test/data/PST130_7067.fa.nto +0 -0
data/test/data/PST130_reverse_primer.csv +1 -0
data/test/data/S22380157.fa +16 -0
data/test/data/S22380157.fa.fai +1 -0
data/test/data/S22380157.vcf +67 -0
data/test/data/S58861868/LIB1716.bam +0 -0
data/test/data/S58861868/LIB1716.sam +651 -0
data/test/data/S58861868/LIB1719.bam +0 -0
data/test/data/S58861868/LIB1719.sam +805 -0
data/test/data/S58861868/LIB1721.bam +0 -0
data/test/data/S58861868/LIB1721.sam +1790 -0
data/test/data/S58861868/LIB1722.bam +0 -0
data/test/data/S58861868/LIB1722.sam +1271 -0
data/test/data/S58861868/S58861868.fa +16 -0
data/test/data/S58861868/S58861868.fa.fai +1 -0
data/test/data/S58861868/S58861868.vcf +76 -0
data/test/data/S58861868/header.txt +9 -0
data/test/data/S58861868/merged.bam +0 -0
data/test/data/S58861868/merged_reheader.bam +0 -0
data/test/data/S58861868/merged_reheader.bam.bai +0 -0
data/test/data/Test3Aspecific.csv +2 -0
data/test/data/Test3Aspecific_contigs.fa +6 -0
data/test/data/bfr_out_test.csv +5 -0
data/test/data/chr1A_C1145499T/chr1A_C1145499T.csv +1 -0
data/test/data/chr1A_G540414846C/chr1A_G540414846C.csv +1 -0
data/test/data/chr1A_G540414846C/chr1A_G540414846C.fa +2 -0
data/test/data/chr1A_T517634750C/chr1A_T517634750C.csv +1 -0
data/test/data/chr2D_C112180134A/chr2D_C112180134A.csv +1 -0
data/test/data/chr4D_C14473543T/chr4D_C14473543T.csv +1 -0
data/test/data/chr4D_C14473543T/chr4D_C14473543T.fa +2 -0
data/test/data/headerMergeed.txt +9 -0
data/test/data/headerS2238015 +1 -0
data/test/data/mergedLibs.bam +0 -0
data/test/data/mergedLibsReheader.bam +0 -0
data/test/data/mergedLibsSorted.bam +0 -0
data/test/data/mergedLibsSorted.bam.bai +0 -0
data/test/data/patological_cases5D.csv +1 -0
data/test/data/primer_3_input_header_test +5 -0
data/test/data/short_primer_design_test.csv +10 -0
data/test/data/some_tests/some_tests.csv +201 -0
data/test/data/test_from_mutant.csv +3 -0
data/test/data/test_iselect.csv +196 -0
data/test/data/test_iselect_reference.fa +1868 -0
data/test/data/test_iselect_reference.fa.fai +934 -0
data/test/data/test_primer3_error.csv +4 -0
data/test/data/test_primer3_error_contigs.fa +10 -0
data/test/test_bfr.rb +135 -0
data/test/test_blast.rb +47 -0
data/test/test_exon_container.rb +17 -0
data/test/test_exonearate.rb +48 -0
data/test/test_integration.rb +76 -0
data/test/test_snp_parsing.rb +121 -0
data/test/test_wrong_selection.sh +5 -0
metadata +356 -0

data/conf/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

data/conf/primer3_config/interpretations/stackmm_i_mm.ds ADDED Viewed

@@ -0,0 +1,256 @@
+AA_AA	inf
+AA_AC	inf
+AA_AG	inf
+AA_AT	12.9
+AA_CA	inf
+AA_CC	inf
+AA_CG	inf
+AA_CT	20.2
+AA_GA	inf
+AA_GC	inf
+AA_GG	inf
+AA_GT	7.4
+AA_TA	1.7
+AA_TC	4.6
+AA_TG	-2.3
+AA_TT	inf
+AC_AA	inf
+AC_AC	inf
+AC_AG	-9.8
+AC_AT	inf
+AC_CA	inf
+AC_CC	inf
+AC_CG	-3.8
+AC_CT	inf
+AC_GA	inf
+AC_GC	inf
+AC_GG	3.2
+AC_GT	inf
+AC_TA	14.6
+AC_TC	-4.4
+AC_TG	inf
+AC_TT	0.2
+AG_AA	inf
+AG_AC	-4.2
+AG_AG	inf
+AG_AT	inf
+AG_CA	inf
+AG_CC	0.6
+AG_CG	inf
+AG_CT	inf
+AG_GA	inf
+AG_GC	-13.2
+AG_GG	inf
+AG_GT	inf
+AG_TA	-2.3
+AG_TC	inf
+AG_TG	-9.5
+AG_TT	0.9
+AT_AA	1.7
+AT_AC	inf
+AT_AG	inf
+AT_AT	inf
+AT_CA	14.6
+AT_CC	inf
+AT_CG	inf
+AT_CT	inf
+AT_GA	-2.3
+AT_GC	inf
+AT_GG	inf
+AT_GT	inf
+AT_TA	inf
+AT_TC	-6.2
+AT_TG	-8.3
+AT_TT	-10.8
+CA_AA	inf
+CA_AC	inf
+CA_AG	inf
+CA_AT	8.0
+CA_CA	inf
+CA_CC	inf
+CA_CG	inf
+CA_CT	16.4
+CA_GA	-4.2
+CA_GC	3.7
+CA_GG	-2.3
+CA_GT	inf
+CA_TA	inf
+CA_TC	inf
+CA_TG	inf
+CA_TT	0.7
+CC_AA	inf
+CC_AC	inf
+CC_AG	14.2
+CC_AT	inf
+CC_CA	inf
+CC_CC	inf
+CC_CG	8.9
+CC_CT	inf
+CC_GA	-0.6
+CC_GC	-7.2
+CC_GG	-19.9
+CC_GT	-4.5
+CC_TA	inf
+CC_TC	inf
+CC_TG	13.5
+CC_TT	inf
+CG_AA	inf
+CG_AC	3.7
+CG_AG	inf
+CG_AT	inf
+CG_CA	inf
+CG_CC	-7.2
+CG_CG	inf
+CG_CT	inf
+CG_GA	-13.2
+CG_GC	inf
+CG_GG	-15.3
+CG_GT	-11.7
+CG_TA	inf
+CG_TC	-6.1
+CG_TG	inf
+CG_TT	inf
+CT_AA	4.6
+CT_AC	inf
+CT_AG	inf
+CT_AT	inf
+CT_CA	-4.4
+CT_CC	inf
+CT_CG	inf
+CT_CT	inf
+CT_GA	inf
+CT_GC	-6.1
+CT_GG	-8.0
+CT_GT	-15.8
+CT_TA	-6.2
+CT_TC	inf
+CT_TG	inf
+CT_TT	inf
+GA_AA	inf
+GA_AC	inf
+GA_AG	inf
+GA_AT	0.7
+GA_CA	-9.8
+GA_CC	14.2
+GA_CG	-1.0
+GA_CT	inf
+GA_GA	inf
+GA_GC	inf
+GA_GG	inf
+GA_GT	3.6
+GA_TA	inf
+GA_TC	inf
+GA_TG	inf
+GA_TT	-5.3
+GC_AA	inf
+GC_AC	inf
+GC_AG	-1.0
+GC_AT	inf
+GC_CA	-3.8
+GC_CC	8.9
+GC_CG	inf
+GC_CT	5.4
+GC_GA	inf
+GC_GC	inf
+GC_GG	-15.8
+GC_GT	inf
+GC_TA	inf
+GC_TC	inf
+GC_TG	-12.3
+GC_TT	inf
+GG_AA	inf
+GG_AC	-2.3
+GG_AG	inf
+GG_AT	inf
+GG_CA	3.2
+GG_CC	-19.9
+GG_CG	-15.8
+GG_CT	10.4
+GG_GA	inf
+GG_GC	-15.3
+GG_GG	inf
+GG_GT	inf
+GG_TA	inf
+GG_TC	80
+GG_TG	inf
+GG_TT	16.3
+GT_AA	23
+GT_AC	inf
+GT_AG	inf
+GT_AT	inf
+GT_CA	inf
+GT_CC	13.5
+GT_CG	-12.3
+GT_CT	-8.4
+GT_GA	-9.5
+GT_GC	inf
+GT_GG	inf
+GT_GT	inf
+GT_TA	-8.3
+GT_TC	inf
+GT_TG	9.5
+GT_TT	inf
+TA_AA	12.9
+TA_AC	8.0
+TA_AG	0.7
+TA_AT	inf
+TA_CA	inf
+TA_CC	inf
+TA_CG	inf
+TA_CT	0.7
+TA_GA	inf
+TA_GC	inf
+TA_GG	inf
+TA_GT	-1.7
+TA_TA	inf
+TA_TC	inf
+TA_TG	inf
+TA_TT	-1.5
+TC_AA	20.2
+TC_AC	16.4
+TC_AG	inf
+TC_AT	0.7
+TC_CA	inf
+TC_CC	inf
+TC_CG	5.4
+TC_CT	inf
+TC_GA	inf
+TC_GC	inf
+TC_GG	10.4
+TC_GT	inf
+TC_TA	inf
+TC_TC	inf
+TC_TG	-8.4
+TC_TT	inf
+TG_AA	7.4
+TG_AC	inf
+TG_AG	3.6
+TG_AT	-1.7
+TG_CA	inf
+TG_CC	-4.5
+TG_CG	inf
+TG_CT	inf
+TG_GA	inf
+TG_GC	-11.7
+TG_GG	inf
+TG_GT	-6.2
+TG_TA	inf
+TG_TC	-15.8
+TG_TG	inf
+TG_TT	inf
+TT_AA	inf
+TT_AC	-7
+TT_AG	-5.3
+TT_AT	-1.5
+TT_CA	0.2
+TT_CC	inf
+TT_CG	inf
+TT_CT	inf
+TT_GA	0.9
+TT_GC	inf
+TT_GG	16.3
+TT_GT	inf
+TT_TA	-10.8
+TT_TC	inf
+TT_TG	inf
+TT_TT	inf

data/conf/primer3_config/interpretations/tetraloop_i.dh ADDED Viewed

@@ -0,0 +1,79 @@
+/* tetraloop bonuses for GNRA and GNAB kcal/mol*(-10) */
+AAAAAT -5
+AAAACT -7
+AAACAT -10
+ACTTGT 0
+AGAAAT 11
+AGAGAT 11
+AGATAT 15
+AGCAAT 16
+AGCGAT 11
+AGCTTT -2
+AGGAAT 11
+AGGGAT 11
+AGGGGT -5
+AGTAAT 16
+AGTGAT 11
+AGTTCT -8
+ATTCGT 2
+ATTTGT 0
+ATTTTT 5
+CAAAAG -5
+CAAACG -7
+CAACAG -10
+CAACCG 0
+CCTTGG 0
+CGAAAG 11
+CGAGAG 11
+CGATAG 15
+CGCAAG 16
+CGCGAG 11
+CGCTTG -2
+CGGAAG 11
+CGGGAG 10
+CGGGGG -5
+CGTAAG 16
+CGTGAG 11
+CGTTCG -8
+CTTCGG 2
+CTTTGG 0
+CTTTTG 5
+GAAAAC -5
+GAAACC -7
+GAACAC -10
+GCTTGC 0
+GGAAAC 11
+GGAGAC 11
+GGATAC 16
+GGCAAC 16
+GGCGAC 11
+GGCTTC -2
+GGGAAC 11
+GGGGAC 11
+GGGGGC -5
+GGTAAC 16
+GGTGAC 11
+GGTTCC -8
+GTTCGC 2
+GTTTGC 0
+GTTTTC 5
+TAAAAA -5
+TAAACA -7
+TAACAA -10
+TCTTGA 0
+TGAAAA 11
+TGAGAA 11
+TGATAA 16
+TGCAAA 16
+TGCGAA 11
+TGCTTA -2
+TGGAAA 11
+TGGGAA 11
+TGGGGA -5
+TGTAAA 16
+TGTGAA 11
+TGTTCA -8
+TTTCGA 2
+TTTTGA 0
+TTTTTA 5

data/conf/primer3_config/interpretations/tetraloop_i.ds ADDED Viewed

@@ -0,0 +1,81 @@
+/*
+VIIDE
+ */
+AAAAAT 6.5
+AAAACT -16.1
+AAACAT -16.1
+ACTTGT -41.9
+AGAAAT -16.1
+AGAGAT -16.1
+AGATAT -16.1
+AGCAAT -16.1
+AGCGAT -16.1
+AGCTTT -16.1
+AGGAAT -16.1
+AGGGAT -16.1
+AGGGGT -6.4
+AGTAAT -16.1
+AGTGAT -16.1
+AGTTCT -16.1
+ATTCGT -16.1
+ATTTGT -16.1
+ATTTTT -16.1
+CAAAAG 12.9
+CAAACG 0
+CAACAG 0
+CAACCG 0
+CCTTGG -25.7
+CGAAAG 0
+CGAGAG 0
+CGATAG 0
+CGCAAG 0
+CGCGAG 0
+CGCTTG 0
+CGGAAG 0
+CGGGAG 0
+CGGGGG 9.7
+CGTAAG 0
+CGTGAG 0
+CGTTCG 0
+CTTCGG 0
+CTTTGG 0
+CTTTTG 0
+GAAAAC 32.3
+GAAACC 0
+GAACAC 0
+GCTTGC -25.7
+GGAAAC 0
+GGAGAC 0
+GGATAC 0
+GGCAAC 0
+GGCGAC 0
+GGCTTC 0
+GGGAAC 0
+GGGGAC 0
+GGGGGC 9.7
+GGTAAC 0
+GGTGAC 0
+GGTTCC 0
+GTTCGC 0
+GTTTGC 0
+GTTTTC 0
+TAAAAA -3.2
+TAAACA -16.1
+TAACAA -16.1
+TCTTGA -41.9
+TGAAAA -16.1
+TGAGAA -16.1
+TGATAA -16.1
+TGCAAA -16.1
+TGCGAA -16.1
+TGCTTA -16.1
+TGGAAA -16.1
+TGGGAA -16.1
+TGGGGA -6.4
+TGTAAA -16.1
+TGTGAA -16.1
+TGTTCA -16.1
+TTTCGA -16.1
+TTTTGA -16.1
+TTTTTA -16.1

data/conf/primer3_config/interpretations/triloop_i.dh ADDED Viewed

@@ -0,0 +1,21 @@
+/* triloop bonus*/
+/* Enthalpy Hairpin loop */
+AGAAT 15
+AGCAT 15
+AGGAT 15
+AGTAT 15
+CGAAG 20
+CGCAG 20
+CGGAG 20
+CGTAG 20
+GGAAC 20
+GGCAC 20
+GGGAC 20
+GGTAC 20
+TGAAA 15
+TGCAA 15
+TGGAA 15
+TGTAA 15

data/conf/primer3_config/interpretations/triloop_i.ds ADDED Viewed

@@ -0,0 +1,18 @@
+/* bonuses for GNA triloops */
+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