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/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_AG -8000
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+AC_GG -4600
+AC_GT 0
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+AC_TC -100
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+AG_AA 0
+AG_AC -4300
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+AG_TT -3200
+AT_AA -3100
+AT_AC 0
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+AT_GA -2500
+AT_GC 0
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+AT_TC -2300
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+CA_AA 0
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+CA_CA 0
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+CA_GC -2600
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+CA_TA 0
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+CC_AA 0
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+GA_AA 0
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+GA_AT -2000
+GA_CA -8000
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+GA_CT -6000
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+GA_GT -1100
+GA_TA 0
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+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
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+TC_CG -4900
+TC_CT 0
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+TC_GG -5700
+TC_GT 0
+TC_TA 0
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+TC_TG -7400
+TC_TT 0
+TG_AA -2400
+TG_AC -6000
+TG_AG -1100
+TG_AT -3900
+TG_CA 0
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+TG_CG 0
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+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
+TT_CA -900
+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
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