bio-twobit 0.2.0 → 0.2.1

Sign up to get free protection for your applications and to get access to all the features.
Files changed (104) hide show
  1. checksums.yaml +4 -4
  2. data/lib/bio/twobit/references/ailmel1.rb +16 -0
  3. data/lib/bio/twobit/references/allmis1.rb +16 -0
  4. data/lib/bio/twobit/references/anocar2.rb +16 -0
  5. data/lib/bio/twobit/references/anogam3.rb +16 -0
  6. data/lib/bio/twobit/references/apimel2.rb +16 -0
  7. data/lib/bio/twobit/references/aplcal1.rb +16 -0
  8. data/lib/bio/twobit/references/aptman1.rb +16 -0
  9. data/lib/bio/twobit/references/aquchr2.rb +16 -0
  10. data/lib/bio/twobit/references/balacu1.rb +16 -0
  11. data/lib/bio/twobit/references/bostau7.rb +16 -0
  12. data/lib/bio/twobit/references/braflo1.rb +16 -0
  13. data/lib/bio/twobit/references/caejap1.rb +16 -0
  14. data/lib/bio/twobit/references/caepb2.rb +16 -0
  15. data/lib/bio/twobit/references/caerem3.rb +16 -0
  16. data/lib/bio/twobit/references/caljac4.rb +16 -0
  17. data/lib/bio/twobit/references/calmil1.rb +16 -0
  18. data/lib/bio/twobit/references/canfam4.rb +16 -0
  19. data/lib/bio/twobit/references/canfam6.rb +16 -0
  20. data/lib/bio/twobit/references/cb3.rb +16 -0
  21. data/lib/bio/twobit/references/ce11.rb +16 -0
  22. data/lib/bio/twobit/references/cersim1.rb +16 -0
  23. data/lib/bio/twobit/references/chlsab2.rb +16 -0
  24. data/lib/bio/twobit/references/chohof1.rb +16 -0
  25. data/lib/bio/twobit/references/chrpic1.rb +16 -0
  26. data/lib/bio/twobit/references/ci2.rb +16 -0
  27. data/lib/bio/twobit/references/crigrichov2.rb +16 -0
  28. data/lib/bio/twobit/references/dasnov3.rb +16 -0
  29. data/lib/bio/twobit/references/dipord1.rb +16 -0
  30. data/lib/bio/twobit/references/dp3.rb +16 -0
  31. data/lib/bio/twobit/references/droana2.rb +16 -0
  32. data/lib/bio/twobit/references/droere1.rb +16 -0
  33. data/lib/bio/twobit/references/drogri1.rb +16 -0
  34. data/lib/bio/twobit/references/dromoj2.rb +16 -0
  35. data/lib/bio/twobit/references/droper1.rb +16 -0
  36. data/lib/bio/twobit/references/drosec1.rb +16 -0
  37. data/lib/bio/twobit/references/drosim1.rb +16 -0
  38. data/lib/bio/twobit/references/drovir2.rb +16 -0
  39. data/lib/bio/twobit/references/droyak2.rb +16 -0
  40. data/lib/bio/twobit/references/ebovir3.rb +16 -0
  41. data/lib/bio/twobit/references/echtel2.rb +16 -0
  42. data/lib/bio/twobit/references/equcab3.rb +16 -0
  43. data/lib/bio/twobit/references/erieur2.rb +16 -0
  44. data/lib/bio/twobit/references/felcat9.rb +16 -0
  45. data/lib/bio/twobit/references/fr2.rb +16 -0
  46. data/lib/bio/twobit/references/gadmor1.rb +16 -0
  47. data/lib/bio/twobit/references/galgal6.rb +16 -0
  48. data/lib/bio/twobit/references/geofor1.rb +16 -0
  49. data/lib/bio/twobit/references/gorgor6.rb +16 -0
  50. data/lib/bio/twobit/references/hetgla2.rb +16 -0
  51. data/lib/bio/twobit/references/latcha1.rb +16 -0
  52. data/lib/bio/twobit/references/loxafr3.rb +16 -0
  53. data/lib/bio/twobit/references/maceug2.rb +16 -0
  54. data/lib/bio/twobit/references/macfas5.rb +16 -0
  55. data/lib/bio/twobit/references/manpen1.rb +16 -0
  56. data/lib/bio/twobit/references/melgal1.rb +16 -0
  57. data/lib/bio/twobit/references/melund1.rb +16 -0
  58. data/lib/bio/twobit/references/micmur2.rb +16 -0
  59. data/lib/bio/twobit/references/mondom5.rb +16 -0
  60. data/lib/bio/twobit/references/myoluc2.rb +16 -0
  61. data/lib/bio/twobit/references/nanpar1.rb +16 -0
  62. data/lib/bio/twobit/references/naslar1.rb +16 -0
  63. data/lib/bio/twobit/references/neosch1.rb +16 -0
  64. data/lib/bio/twobit/references/nomleu3.rb +16 -0
  65. data/lib/bio/twobit/references/ochpri3.rb +16 -0
  66. data/lib/bio/twobit/references/orenil2.rb +16 -0
  67. data/lib/bio/twobit/references/ornana2.rb +16 -0
  68. data/lib/bio/twobit/references/orycun2.rb +16 -0
  69. data/lib/bio/twobit/references/orylat2.rb +16 -0
  70. data/lib/bio/twobit/references/otogar3.rb +16 -0
  71. data/lib/bio/twobit/references/oviari4.rb +16 -0
  72. data/lib/bio/twobit/references/panpan3.rb +16 -0
  73. data/lib/bio/twobit/references/pantro6.rb +16 -0
  74. data/lib/bio/twobit/references/papanu4.rb +16 -0
  75. data/lib/bio/twobit/references/papham1.rb +16 -0
  76. data/lib/bio/twobit/references/petmar3.rb +16 -0
  77. data/lib/bio/twobit/references/ponabe2.rb +16 -0
  78. data/lib/bio/twobit/references/ponabe3.rb +16 -0
  79. data/lib/bio/twobit/references/pripac1.rb +16 -0
  80. data/lib/bio/twobit/references/procap1.rb +16 -0
  81. data/lib/bio/twobit/references/ptevam1.rb +16 -0
  82. data/lib/bio/twobit/references/rhemac10.rb +16 -0
  83. data/lib/bio/twobit/references/rn6.rb +16 -0
  84. data/lib/bio/twobit/references/saccer3.rb +16 -0
  85. data/lib/bio/twobit/references/saibol1.rb +16 -0
  86. data/lib/bio/twobit/references/sarhar1.rb +16 -0
  87. data/lib/bio/twobit/references/sorara2.rb +16 -0
  88. data/lib/bio/twobit/references/spetri2.rb +16 -0
  89. data/lib/bio/twobit/references/strpur2.rb +16 -0
  90. data/lib/bio/twobit/references/susscr11.rb +16 -0
  91. data/lib/bio/twobit/references/taegut2.rb +16 -0
  92. data/lib/bio/twobit/references/tarsyr2.rb +16 -0
  93. data/lib/bio/twobit/references/tetnig2.rb +16 -0
  94. data/lib/bio/twobit/references/thasir1.rb +16 -0
  95. data/lib/bio/twobit/references/triman1.rb +16 -0
  96. data/lib/bio/twobit/references/tupbel1.rb +16 -0
  97. data/lib/bio/twobit/references/turtru2.rb +16 -0
  98. data/lib/bio/twobit/references/uusfur1.rb +16 -0
  99. data/lib/bio/twobit/references/vicpac2.rb +16 -0
  100. data/lib/bio/twobit/references/wuhcor1.rb +16 -0
  101. data/lib/bio/twobit/references/xentro10.rb +16 -0
  102. data/lib/bio/twobit/version.rb +1 -1
  103. data/lib/bio/twobit.rb +2 -16
  104. metadata +103 -3
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class PapHam1 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "papHam1"
9
+ @metadata.name = "papHam1"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/papHam1/bigZips/papHam1.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class PetMar3 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "petMar3"
9
+ @metadata.name = "petMar3"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/petMar3/bigZips/petMar3.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class PonAbe2 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "ponAbe2"
9
+ @metadata.name = "ponAbe2"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/ponAbe2/bigZips/ponAbe2.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class PonAbe3 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "ponAbe3"
9
+ @metadata.name = "ponAbe3"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/ponAbe3/bigZips/ponAbe3.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class PriPac1 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "priPac1"
9
+ @metadata.name = "priPac1"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/priPac1/bigZips/priPac1.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class ProCap1 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "proCap1"
9
+ @metadata.name = "proCap1"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/proCap1/bigZips/proCap1.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class PteVam1 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "pteVam1"
9
+ @metadata.name = "pteVam1"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/pteVam1/bigZips/pteVam1.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class RheMac10 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "rheMac10"
9
+ @metadata.name = "rheMac10"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/rheMac10/bigZips/rheMac10.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class Rn6 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "rn6"
9
+ @metadata.name = "rn6"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/rn6/bigZips/rn6.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class SacCer3 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "sacCer3"
9
+ @metadata.name = "sacCer3"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/bigZips/sacCer3.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class SaiBol1 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "saiBol1"
9
+ @metadata.name = "saiBol1"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/saiBol1/bigZips/saiBol1.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class SarHar1 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "sarHar1"
9
+ @metadata.name = "sarHar1"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/sarHar1/bigZips/sarHar1.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class SorAra2 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "sorAra2"
9
+ @metadata.name = "sorAra2"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/sorAra2/bigZips/sorAra2.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class SpeTri2 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "speTri2"
9
+ @metadata.name = "speTri2"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/speTri2/bigZips/speTri2.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class StrPur2 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "strPur2"
9
+ @metadata.name = "strPur2"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/strPur2/bigZips/strPur2.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class SusScr11 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "susScr11"
9
+ @metadata.name = "susScr11"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/susScr11/bigZips/susScr11.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class TaeGut2 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "taeGut2"
9
+ @metadata.name = "taeGut2"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/taeGut2/bigZips/taeGut2.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class TarSyr2 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "tarSyr2"
9
+ @metadata.name = "tarSyr2"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/tarSyr2/bigZips/tarSyr2.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class TetNig2 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "tetNig2"
9
+ @metadata.name = "tetNig2"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/tetNig2/bigZips/tetNig2.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class ThaSir1 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "thaSir1"
9
+ @metadata.name = "thaSir1"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/thaSir1/bigZips/thaSir1.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class TriMan1 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "triMan1"
9
+ @metadata.name = "triMan1"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/triMan1/bigZips/triMan1.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class TupBel1 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "tupBel1"
9
+ @metadata.name = "tupBel1"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/tupBel1/bigZips/tupBel1.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class TurTru2 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "turTru2"
9
+ @metadata.name = "turTru2"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/turTru2/bigZips/turTru2.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class UusFur1 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "uusFur1"
9
+ @metadata.name = "uusFur1"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/uusFur1/bigZips/uusFur1.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class VicPac2 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "vicPac2"
9
+ @metadata.name = "vicPac2"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/vicPac2/bigZips/vicPac2.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class WuhCor1 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "wuhCor1"
9
+ @metadata.name = "wuhCor1"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/bigZips/wuhCor1.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -0,0 +1,16 @@
1
+ require_relative "../reference_genome"
2
+
3
+ module Bio
4
+ class TwoBit
5
+ class XenTro10 < ReferenceGenome
6
+ def initialize(**kwargs)
7
+ @metadata = Metadata.new
8
+ @metadata.id = "xenTro10"
9
+ @metadata.name = "xenTro10"
10
+ @metadata.url = "https://hgdownload.soe.ucsc.edu/downloads.html"
11
+ @data_url = "https://hgdownload.soe.ucsc.edu/goldenPath/xenTro10/bigZips/xenTro10.2bit"
12
+ super(**kwargs)
13
+ end
14
+ end
15
+ end
16
+ end
@@ -2,6 +2,6 @@
2
2
 
3
3
  module Bio
4
4
  class TwoBit
5
- VERSION = "0.2.0"
5
+ VERSION = "0.2.1"
6
6
  end
7
7
  end
data/lib/bio/twobit.rb CHANGED
@@ -24,22 +24,6 @@ module Bio
24
24
  end
25
25
  file
26
26
  end
27
-
28
- # Here, const_missing is used instead of autoload.
29
-
30
- def const_missing(name)
31
- # prevents const_get from being called recursively many times.
32
- @missing_const ||= []
33
- super if @missing_const.include? name
34
- @missing_const << name
35
-
36
- path = File.join(__dir__, "twobit/references", "#{name.to_s.downcase}.rb")
37
- if File.exist?(path)
38
- require path
39
- return const_get(name)
40
- end
41
- super
42
- end
43
27
  end
44
28
 
45
29
  def initialize(fname, masked: false)
@@ -117,3 +101,5 @@ module Bio
117
101
  end
118
102
  end
119
103
  end
104
+
105
+ Dir[__dir__ + "/twobit/references/*.rb"].each { |file| require file }
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bio-twobit
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.2.0
4
+ version: 0.2.1
5
5
  platform: ruby
6
6
  authors:
7
7
  - kojix2
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2023-01-11 00:00:00.000000000 Z
11
+ date: 2023-01-12 00:00:00.000000000 Z
12
12
  dependencies: []
13
13
  description: This is a Ruby binding for lib2bit(https://github.com/dpryan79/lib2bit),
14
14
  which provides high-speed access to genomic data in 2bit file format.
@@ -32,15 +32,115 @@ files:
32
32
  - lib/bio/twobit/downloader.rb
33
33
  - lib/bio/twobit/metadata.rb
34
34
  - lib/bio/twobit/reference_genome.rb
35
+ - lib/bio/twobit/references/ailmel1.rb
36
+ - lib/bio/twobit/references/allmis1.rb
37
+ - lib/bio/twobit/references/anocar2.rb
38
+ - lib/bio/twobit/references/anogam3.rb
39
+ - lib/bio/twobit/references/apimel2.rb
40
+ - lib/bio/twobit/references/aplcal1.rb
41
+ - lib/bio/twobit/references/aptman1.rb
42
+ - lib/bio/twobit/references/aquchr2.rb
43
+ - lib/bio/twobit/references/balacu1.rb
44
+ - lib/bio/twobit/references/bostau7.rb
45
+ - lib/bio/twobit/references/braflo1.rb
46
+ - lib/bio/twobit/references/caejap1.rb
47
+ - lib/bio/twobit/references/caepb2.rb
48
+ - lib/bio/twobit/references/caerem3.rb
49
+ - lib/bio/twobit/references/caljac4.rb
50
+ - lib/bio/twobit/references/calmil1.rb
51
+ - lib/bio/twobit/references/canfam4.rb
52
+ - lib/bio/twobit/references/canfam6.rb
53
+ - lib/bio/twobit/references/cb3.rb
54
+ - lib/bio/twobit/references/ce11.rb
55
+ - lib/bio/twobit/references/cersim1.rb
56
+ - lib/bio/twobit/references/chlsab2.rb
57
+ - lib/bio/twobit/references/chohof1.rb
58
+ - lib/bio/twobit/references/chrpic1.rb
59
+ - lib/bio/twobit/references/ci2.rb
60
+ - lib/bio/twobit/references/crigrichov2.rb
35
61
  - lib/bio/twobit/references/danrer10.rb
36
62
  - lib/bio/twobit/references/danrer11.rb
63
+ - lib/bio/twobit/references/dasnov3.rb
64
+ - lib/bio/twobit/references/dipord1.rb
37
65
  - lib/bio/twobit/references/dm6.rb
66
+ - lib/bio/twobit/references/dp3.rb
67
+ - lib/bio/twobit/references/droana2.rb
68
+ - lib/bio/twobit/references/droere1.rb
69
+ - lib/bio/twobit/references/drogri1.rb
70
+ - lib/bio/twobit/references/dromoj2.rb
71
+ - lib/bio/twobit/references/droper1.rb
72
+ - lib/bio/twobit/references/drosec1.rb
73
+ - lib/bio/twobit/references/drosim1.rb
74
+ - lib/bio/twobit/references/drovir2.rb
75
+ - lib/bio/twobit/references/droyak2.rb
76
+ - lib/bio/twobit/references/ebovir3.rb
77
+ - lib/bio/twobit/references/echtel2.rb
78
+ - lib/bio/twobit/references/equcab3.rb
79
+ - lib/bio/twobit/references/erieur2.rb
80
+ - lib/bio/twobit/references/felcat9.rb
81
+ - lib/bio/twobit/references/fr2.rb
82
+ - lib/bio/twobit/references/gadmor1.rb
83
+ - lib/bio/twobit/references/galgal6.rb
84
+ - lib/bio/twobit/references/geofor1.rb
85
+ - lib/bio/twobit/references/gorgor6.rb
86
+ - lib/bio/twobit/references/hetgla2.rb
38
87
  - lib/bio/twobit/references/hg19.rb
39
88
  - lib/bio/twobit/references/hg38.rb
40
89
  - lib/bio/twobit/references/hs1.rb
90
+ - lib/bio/twobit/references/latcha1.rb
91
+ - lib/bio/twobit/references/loxafr3.rb
92
+ - lib/bio/twobit/references/maceug2.rb
93
+ - lib/bio/twobit/references/macfas5.rb
94
+ - lib/bio/twobit/references/manpen1.rb
95
+ - lib/bio/twobit/references/melgal1.rb
96
+ - lib/bio/twobit/references/melund1.rb
97
+ - lib/bio/twobit/references/micmur2.rb
41
98
  - lib/bio/twobit/references/mm10.rb
42
99
  - lib/bio/twobit/references/mm39.rb
43
100
  - lib/bio/twobit/references/mm9.rb
101
+ - lib/bio/twobit/references/mondom5.rb
102
+ - lib/bio/twobit/references/myoluc2.rb
103
+ - lib/bio/twobit/references/nanpar1.rb
104
+ - lib/bio/twobit/references/naslar1.rb
105
+ - lib/bio/twobit/references/neosch1.rb
106
+ - lib/bio/twobit/references/nomleu3.rb
107
+ - lib/bio/twobit/references/ochpri3.rb
108
+ - lib/bio/twobit/references/orenil2.rb
109
+ - lib/bio/twobit/references/ornana2.rb
110
+ - lib/bio/twobit/references/orycun2.rb
111
+ - lib/bio/twobit/references/orylat2.rb
112
+ - lib/bio/twobit/references/otogar3.rb
113
+ - lib/bio/twobit/references/oviari4.rb
114
+ - lib/bio/twobit/references/panpan3.rb
115
+ - lib/bio/twobit/references/pantro6.rb
116
+ - lib/bio/twobit/references/papanu4.rb
117
+ - lib/bio/twobit/references/papham1.rb
118
+ - lib/bio/twobit/references/petmar3.rb
119
+ - lib/bio/twobit/references/ponabe2.rb
120
+ - lib/bio/twobit/references/ponabe3.rb
121
+ - lib/bio/twobit/references/pripac1.rb
122
+ - lib/bio/twobit/references/procap1.rb
123
+ - lib/bio/twobit/references/ptevam1.rb
124
+ - lib/bio/twobit/references/rhemac10.rb
125
+ - lib/bio/twobit/references/rn6.rb
126
+ - lib/bio/twobit/references/saccer3.rb
127
+ - lib/bio/twobit/references/saibol1.rb
128
+ - lib/bio/twobit/references/sarhar1.rb
129
+ - lib/bio/twobit/references/sorara2.rb
130
+ - lib/bio/twobit/references/spetri2.rb
131
+ - lib/bio/twobit/references/strpur2.rb
132
+ - lib/bio/twobit/references/susscr11.rb
133
+ - lib/bio/twobit/references/taegut2.rb
134
+ - lib/bio/twobit/references/tarsyr2.rb
135
+ - lib/bio/twobit/references/tetnig2.rb
136
+ - lib/bio/twobit/references/thasir1.rb
137
+ - lib/bio/twobit/references/triman1.rb
138
+ - lib/bio/twobit/references/tupbel1.rb
139
+ - lib/bio/twobit/references/turtru2.rb
140
+ - lib/bio/twobit/references/uusfur1.rb
141
+ - lib/bio/twobit/references/vicpac2.rb
142
+ - lib/bio/twobit/references/wuhcor1.rb
143
+ - lib/bio/twobit/references/xentro10.rb
44
144
  - lib/bio/twobit/version.rb
45
145
  homepage: https://github.com/ruby-on-bioc/bio-twobit
46
146
  licenses:
@@ -61,7 +161,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
61
161
  - !ruby/object:Gem::Version
62
162
  version: '0'
63
163
  requirements: []
64
- rubygems_version: 3.4.1
164
+ rubygems_version: 3.3.26
65
165
  signing_key:
66
166
  specification_version: 4
67
167
  summary: A ruby library for accessing 2bit files