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/tstack2_i.dh ADDED Viewed

@@ -0,0 +1,256 @@
+AA_AA 0
+AA_AC 0
+AA_AG 0
+AA_AT -2500
+AA_CA 0
+AA_CC 0
+AA_CG 0
+AA_CT -2700
+AA_GA 0
+AA_GC 0
+AA_GG 0
+AA_GT -2400
+AA_TA -3100
+AA_TC -1600
+AA_TG -1900
+AA_TT -5000
+AC_AA 0
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+AC_GG -4600
+AC_GT 0
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+AC_TC -100
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+AG_AA 0
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+CA_AA 0
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+CC_AA 0
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+GA_AA 0
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+GA_CA -8000
+GA_CC -5000
+GA_CG -4300
+GA_CT -6000
+GA_GA 0
+GA_GC 0
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+GA_GT -1100
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+GA_TT -3600
+GC_AA 0
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+GC_CC -3900
+GC_CG -7000
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+GC_GA 0
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+GC_TC 0
+GC_TG -5900
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+GG_AA 0
+GG_AC -3900
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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
+GG_TA 0
+GG_TC -6600
+GG_TG 0
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+GT_AA -1900
+GT_AC 0
+GT_AG 0
+GT_AT 0
+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
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+TT_AA -5000
+TT_AC -700
+TT_AG -3600
+TT_AT -3200
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+TT_CC 0
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+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/conf/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
+CC_AC inf
+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
+CC_TT inf
+CG_AA inf
+CG_AC -5.9
+CG_AG inf
+CG_AT inf
+CG_CA inf
+CG_CC -5.1
+CG_CG inf
+CG_CT inf
+CG_GA -15.5
+CG_GC -19.3
+CG_GG -9.5
+CG_GT -9.0
+CG_TA inf
+CG_TC -10.6
+CG_TG inf
+CG_TT inf
+CT_AA -4.0
+CT_AC inf
+CT_AG inf
+CT_AT inf
+CT_CA -0.5
+CT_CC inf
+CT_CG inf
+CT_CT inf
+CT_GA -16.1
+CT_GC -10.6
+CT_GG -18.7
+CT_GT -16.9
+CT_TA -6.3
+CT_TC inf
+CT_TG inf
+CT_TT inf
+GA_AA inf
+GA_AC inf
+GA_AG inf
+GA_AT -4.7
+GA_CA -22.5
+GA_CC -13.8
+GA_CG -11.1
+GA_CT -16.1
+GA_GA inf
+GA_GC inf
+GA_GG inf
+GA_GT -2.7
+GA_TA inf
+GA_TC inf
+GA_TG inf
+GA_TT -9.8
+GC_AA inf
+GC_AC inf
+GC_AG -11.1
+GC_AT inf
+GC_CA -7.1
+GC_CC -10.6
+GC_CG -19.3
+GC_CT -13.5
+GC_GA inf
+GC_GC inf
+GC_GG -19.2
+GC_GT inf
+GC_TA inf
+GC_TC inf
+GC_TG -16.1
+GC_TT inf
+GG_AA inf
+GG_AC -9.6
+GG_AG inf
+GG_AT inf
+GG_CA -11.4
+GG_CC -19.3
+GG_CG -19.2
+GG_CT -15.9
+GG_GA inf
+GG_GC -9.5
+GG_GG inf
+GG_GT inf
+GG_TA inf
+GG_TC -18.7
+GG_TG inf
+GG_TT inf
+GT_AA -4.4
+GT_AC inf
+GT_AG inf
+GT_AT inf
+GT_CA -16.1
+GT_CC -7.8
+GT_CG -16.1
+GT_CT -21.2
+GT_GA -2.1
+GT_GC inf
+GT_GG inf
+GT_GT inf
+GT_TA -9.4
+GT_TC inf
+GT_TG inf
+GT_TT inf
+TA_AA -6.3
+TA_AC -5.9
+TA_AG -4.7
+TA_AT -14.2
+TA_CA inf
+TA_CC inf
+TA_CG inf
+TA_CT -6.3
+TA_GA inf
+TA_GC inf
+TA_GG inf
+TA_GT -10.5
+TA_TA inf
+TA_TC inf
+TA_TG inf
+TA_TT -8.9
+TC_AA -7.0
+TC_AC -1.3
+TC_AG -16.1
+TC_AT -6.3
+TC_CA inf
+TC_CC inf
+TC_CG -13.5
+TC_CT inf
+TC_GA inf
+TC_GC inf
+TC_GG -15.9
+TC_GT inf
+TC_TA inf
+TC_TC inf
+TC_TG -21.2
+TC_TT inf
+TG_AA -5.8
+TG_AC -16.1
+TG_AG -2.7
+TG_AT -10.5
+TG_CA inf
+TG_CC -8.0
+TG_CG inf
+TG_CT inf
+TG_GA inf
+TG_GC -9.0
+TG_GG inf
+TG_GT inf
+TG_TA inf
+TG_TC -16.9
+TG_TG inf
+TG_TT inf
+TT_AA -13.5
+TT_AC -1.2
+TT_AG -9.8
+TT_AT -8.9
+TT_CA -1.7
+TT_CC inf
+TT_CG inf
+TT_CT inf
+TT_GA -8.7
+TT_GC inf
+TT_GG inf
+TT_GT inf
+TT_TA -6.5
+TT_TC inf
+TT_TG inf
+TT_TT inf

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

@@ -0,0 +1,256 @@
+AA_AA 0
+AA_AC 0
+AA_AG 0
+AA_AT 25
+AA_CA 0
+AA_CC 0
+AA_CG 0
+AA_CT 27
+AA_GA 0
+AA_GC 0
+AA_GG 0
+AA_GT 24
+AA_TA 31
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