RubyGems - bio-polyploid-tools - Versions diffs - 0.1.0 - Mend

bio-polyploid-tools 0.1.0

Files changed (92) hide show

checksums.yaml +7 -0
data/Gemfile +16 -0
data/Gemfile.lock +67 -0
data/README +21 -0
data/Rakefile +61 -0
data/VERSION +1 -0
data/bin/bfr.rb +133 -0
data/bin/count_variations.rb +36 -0
data/bin/filter_blat_by_target_coverage.rb +15 -0
data/bin/find_best_blat_hit.rb +32 -0
data/bin/hexaploid_primers.rb +168 -0
data/bin/homokaryot_primers.rb +155 -0
data/bin/map_markers_to_contigs.rb +66 -0
data/bin/markers_in_region.rb +42 -0
data/bin/polymarker.rb +219 -0
data/bin/snps_between_bams.rb +106 -0
data/bio-polyploid-tools.gemspec +139 -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 +698 -0
data/lib/bio/BIOExtensions.rb +186 -0
data/lib/bio/PolyploidTools/ChromosomeArm.rb +52 -0
data/lib/bio/PolyploidTools/ExonContainer.rb +194 -0
data/lib/bio/PolyploidTools/Marker.rb +175 -0
data/lib/bio/PolyploidTools/PrimerRegion.rb +22 -0
data/lib/bio/PolyploidTools/SNP.rb +681 -0
data/lib/bio/PolyploidTools/SNPSequence.rb +56 -0
data/lib/bio/SAMToolsExtensions.rb +284 -0
data/lib/bio/db/exonerate.rb +272 -0
data/lib/bio/db/fastadb.rb +164 -0
data/lib/bio/db/primer3.rb +673 -0
data/lib/bioruby-polyploid-tools.rb +25 -0
data/test/data/BS00068396_51.fa +2 -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_exonerate.tab +6 -0
data/test/data/BS00068396_51_genes.txt +14 -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/S22380157.fa +16 -0
data/test/data/S22380157.fa.fai +1 -0
data/test/data/Test3Aspecific.csv +1 -0
data/test/data/Test3Aspecific_contigs.fa +6 -0
data/test/data/patological_cases5D.csv +1 -0
data/test/data/short_primer_design_test.csv +10 -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 +51 -0
data/test/test_exon_container.rb +17 -0
data/test/test_exonearate.rb +53 -0
data/test/test_snp_parsing.rb +40 -0
metadata +201 -0

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

@@ -0,0 +1,256 @@
+AA_AA 0
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+TA_AA 25
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+TT_TA 24
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data/conf/primer3_config/interpretations/tstack_i.ds ADDED

@@ -0,0 +1,256 @@
+AA_AA inf
+AA_AC inf
+AA_AG inf
+AA_AT 63
+AA_CA inf
+AA_CC inf
+AA_CG inf
+AA_CT 70
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