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

bio-polymarker 1.3.2

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 (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