bio-polyploid-tools 0.7.3 → 0.8.0

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Files changed (66) hide show
  1. checksums.yaml +5 -5
  2. data/.travis.yml +17 -0
  3. data/Gemfile +10 -7
  4. data/README.md +44 -0
  5. data/Rakefile +14 -14
  6. data/VERSION +1 -1
  7. data/bin/bfr.rb +2 -2
  8. data/bin/blast_triads.rb +166 -0
  9. data/bin/blast_triads_promoters.rb +192 -0
  10. data/bin/find_homoeologue_variations.rb +385 -0
  11. data/bin/get_longest_hsp_blastx_triads.rb +66 -0
  12. data/bin/hexaploid_primers.rb +2 -2
  13. data/bin/homokaryot_primers.rb +2 -2
  14. data/bin/mafft_triads.rb +120 -0
  15. data/bin/mafft_triads_promoters.rb +403 -0
  16. data/bin/polymarker.rb +73 -17
  17. data/bin/polymarker_capillary.rb +416 -0
  18. data/bin/snp_position_to_polymarker.rb +5 -3
  19. data/bin/snps_between_bams.rb +0 -29
  20. data/bin/vcfLineToTable.rb +56 -0
  21. data/bio-polyploid-tools.gemspec +74 -32
  22. data/lib/bio/BFRTools.rb +1 -0
  23. data/lib/bio/PolyploidTools/ChromosomeArm.rb +2 -6
  24. data/lib/bio/PolyploidTools/ExonContainer.rb +31 -8
  25. data/lib/bio/PolyploidTools/NoSNPSequence.rb +286 -0
  26. data/lib/bio/PolyploidTools/PrimerRegion.rb +9 -1
  27. data/lib/bio/PolyploidTools/SNP.rb +58 -18
  28. data/lib/bio/PolyploidTools/SNPMutant.rb +5 -3
  29. data/lib/bio/db/blast.rb +112 -0
  30. data/lib/bio/db/exonerate.rb +4 -5
  31. data/lib/bio/db/primer3.rb +83 -14
  32. data/test/data/BS00068396_51_blast.tab +4 -0
  33. data/test/data/BS00068396_51_contigs.nhr +0 -0
  34. data/test/data/BS00068396_51_contigs.nin +0 -0
  35. data/test/data/BS00068396_51_contigs.nsq +0 -0
  36. data/test/data/BS00068396_51_for_polymarker.fa +1 -0
  37. data/test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa.fai +11 -0
  38. data/test/data/S22380157.vcf +67 -0
  39. data/test/data/S58861868/LIB1716.bam +0 -0
  40. data/test/data/S58861868/LIB1716.sam +651 -0
  41. data/test/data/S58861868/LIB1719.bam +0 -0
  42. data/test/data/S58861868/LIB1719.sam +805 -0
  43. data/test/data/S58861868/LIB1721.bam +0 -0
  44. data/test/data/S58861868/LIB1721.sam +1790 -0
  45. data/test/data/S58861868/LIB1722.bam +0 -0
  46. data/test/data/S58861868/LIB1722.sam +1271 -0
  47. data/test/data/S58861868/S58861868.fa +16 -0
  48. data/test/data/S58861868/S58861868.fa.fai +1 -0
  49. data/test/data/S58861868/S58861868.vcf +76 -0
  50. data/test/data/S58861868/header.txt +9 -0
  51. data/test/data/S58861868/merged.bam +0 -0
  52. data/test/data/S58861868/merged_reheader.bam +0 -0
  53. data/test/data/S58861868/merged_reheader.bam.bai +0 -0
  54. data/test/data/bfr_out_test.csv +5 -5
  55. data/test/data/headerMergeed.txt +9 -0
  56. data/test/data/headerS2238015 +1 -0
  57. data/test/data/mergedLibs.bam +0 -0
  58. data/test/data/mergedLibsReheader.bam +0 -0
  59. data/test/data/mergedLibsSorted.bam +0 -0
  60. data/test/data/mergedLibsSorted.bam.bai +0 -0
  61. data/test/test_bfr.rb +26 -34
  62. data/test/test_blast.rb +47 -0
  63. data/test/test_exonearate.rb +4 -9
  64. data/test/test_snp_parsing.rb +42 -22
  65. metadata +81 -20
  66. data/Gemfile.lock +0 -67
data/Gemfile.lock DELETED
@@ -1,67 +0,0 @@
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- GEM
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- remote: http://rubygems.org/
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- specs:
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- addressable (2.3.6)
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- atomic (1.1.16)
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- bio (1.4.3.0001)
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- bio-samtools (2.0.4)
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- bio (>= 1.4.2)
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- bio-svgenes (>= 0.4.1)
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- bio-svgenes (0.4.1)
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- builder (3.2.2)
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- descendants_tracker (0.0.4)
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- thread_safe (~> 0.3, >= 0.3.1)
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- faraday (0.9.0)
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- multipart-post (>= 1.2, < 3)
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- git (1.2.6)
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- github_api (0.11.3)
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- addressable (~> 2.3)
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- descendants_tracker (~> 0.0.1)
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- faraday (~> 0.8, < 0.10)
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- hashie (>= 1.2)
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- multi_json (>= 1.7.5, < 2.0)
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- nokogiri (~> 1.6.0)
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- oauth2
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- hashie (2.0.5)
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- highline (1.6.21)
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- jeweler (2.0.1)
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- builder
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- bundler (>= 1.0)
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- git (>= 1.2.5)
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- github_api
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- highline (>= 1.6.15)
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- nokogiri (>= 1.5.10)
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- rake
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- rdoc
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- json (1.8.1)
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- jwt (0.1.11)
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- multi_json (>= 1.5)
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- mini_portile (0.5.3)
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- multi_json (1.9.2)
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- multi_xml (0.5.5)
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- multipart-post (2.0.0)
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- nokogiri (1.6.1)
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- mini_portile (~> 0.5.0)
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- oauth2 (0.9.3)
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- faraday (>= 0.8, < 0.10)
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- jwt (~> 0.1.8)
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- multi_json (~> 1.3)
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- multi_xml (~> 0.5)
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- rack (~> 1.2)
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- rack (1.5.2)
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- rake (10.2.2)
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- rdoc (4.1.1)
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- json (~> 1.4)
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- systemu (2.6.4)
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- thread_safe (0.3.1)
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- atomic (>= 1.1.7, < 2)
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-
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- PLATFORMS
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- ruby
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-
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- DEPENDENCIES
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- bio (>= 1.4.3)
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- bio-samtools (>= 2.0.4)
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- jeweler
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- rake
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- systemu (>= 2.5.2)