neurohmmer 0.1.0

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Files changed (133) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +35 -0
  3. data/CODE_OF_CONDUCT.md +13 -0
  4. data/Gemfile +4 -0
  5. data/LICENSE +662 -0
  6. data/README.md +136 -0
  7. data/Rakefile +17 -0
  8. data/bin/neurohmmer +69 -0
  9. data/data/hmm/CRH_DH44.fa.hmm +427 -0
  10. data/data/hmm/Chordate_Glucagon_PACAP.fa.hmm +484 -0
  11. data/data/hmm/Chordate_Neurotensin_precursors_neurotensin_like_Ciona.fa.hmm +526 -0
  12. data/data/hmm/Deutrostomian_tachykinin.fa.hmm +367 -0
  13. data/data/hmm/Gastrin_releasing_peptide.fa.hmm +448 -0
  14. data/data/hmm/GnRH.fa.hmm +370 -0
  15. data/data/hmm/Hypocretin_orexin.fa.hmm +451 -0
  16. data/data/hmm/Lophotrochozoan_luqin_arthropod_RYamide.fa.hmm +385 -0
  17. data/data/hmm/NPFF.fa.hmm +430 -0
  18. data/data/hmm/NPS.fa.hmm +790 -0
  19. data/data/hmm/PTH.fa.hmm +502 -0
  20. data/data/hmm/Protostomian_Allatostatin_B.fa.hmm +835 -0
  21. data/data/hmm/Protostomian_CCH_amide.fa.hmm +415 -0
  22. data/data/hmm/Protostomian_Ecdysis_Triggering_Hormone.fa.hmm +433 -0
  23. data/data/hmm/Protostomian_PDF.fa.hmm +265 -0
  24. data/data/hmm/Protostomian_allatostatin_C.fa.hmm +352 -0
  25. data/data/hmm/Protostomian_proctolin.fa.hmm +346 -0
  26. data/data/hmm/Putative_chordate_Opioid.fa.hmm +802 -0
  27. data/data/hmm/SIF.fa.hmm +286 -0
  28. data/data/hmm/TRH.fa.hmm +910 -0
  29. data/data/hmm/allatotropin.fa.hmm +433 -0
  30. data/data/hmm/ambulacrarian_amphioxus_NPS-like.fa.hmm +847 -0
  31. data/data/hmm/avp.fa.hmm +475 -0
  32. data/data/hmm/calcitonin_DH31.fa.hmm +418 -0
  33. data/data/hmm/cholecystokinin_sulfakinin.fa.hmm +433 -0
  34. data/data/hmm/chordate_OX26_QRFP.fa.hmm +475 -0
  35. data/data/hmm/chordate_somatostatin_cortistatin_like.fa.hmm +361 -0
  36. data/data/hmm/f_type_SALMF.fa.hmm +811 -0
  37. data/data/hmm/galanin.fa.hmm +391 -0
  38. data/data/hmm/l_type_SALMF.fa.hmm +523 -0
  39. data/data/hmm/nmu_pyrokinin.fa.hmm +424 -0
  40. data/data/hmm/npy_npf.fa.hmm +301 -0
  41. data/data/hmm/protostomian_CCAP.fa.hmm +415 -0
  42. data/data/hmm/protostomian_allatostatinA_buccalin.fa.hmm +706 -0
  43. data/data/hmm/protostomian_leucokinin.fa.hmm +511 -0
  44. data/data/hmm/protostomian_tackykinin.fa.hmm +760 -0
  45. data/data/hmm/tachykinin.fa.hmm +541 -0
  46. data/data/hmm/vertebrate_ghrelin_motilin.fa.hmm +382 -0
  47. data/data/raw_data/CRH_DH44.fa +44 -0
  48. data/data/raw_data/CRH_DH44.fa.aligned.fa +242 -0
  49. data/data/raw_data/Chordate_Glucagon_PACAP.fa +18 -0
  50. data/data/raw_data/Chordate_Glucagon_PACAP.fa.aligned.fa +72 -0
  51. data/data/raw_data/Chordate_Neurotensin_precursors_neurotensin_like_Ciona.fa +10 -0
  52. data/data/raw_data/Chordate_Neurotensin_precursors_neurotensin_like_Ciona.fa.aligned.fa +25 -0
  53. data/data/raw_data/Deutrostomian_tachykinin.fa +1283 -0
  54. data/data/raw_data/Deutrostomian_tachykinin.fa.aligned.fa +5707 -0
  55. data/data/raw_data/Gastrin_releasing_peptide.fa +12 -0
  56. data/data/raw_data/Gastrin_releasing_peptide.fa.aligned.fa +25 -0
  57. data/data/raw_data/GnRH.fa +22 -0
  58. data/data/raw_data/GnRH.fa.aligned.fa +66 -0
  59. data/data/raw_data/Hypocretin_orexin.fa +14 -0
  60. data/data/raw_data/Hypocretin_orexin.fa.aligned.fa +49 -0
  61. data/data/raw_data/Lophotrochozoan_luqin_arthropod_RYamide.fa +26 -0
  62. data/data/raw_data/Lophotrochozoan_luqin_arthropod_RYamide.fa.aligned.fa +91 -0
  63. data/data/raw_data/NPFF.fa +16 -0
  64. data/data/raw_data/NPFF.fa.aligned.fa +48 -0
  65. data/data/raw_data/NPS.fa +8 -0
  66. data/data/raw_data/NPS.fa.aligned.fa +24 -0
  67. data/data/raw_data/PTH.fa +24 -0
  68. data/data/raw_data/PTH.fa.aligned.fa +144 -0
  69. data/data/raw_data/Protostomian_Allatostatin_B.fa +17 -0
  70. data/data/raw_data/Protostomian_Allatostatin_B.fa.aligned.fa +120 -0
  71. data/data/raw_data/Protostomian_CCH_amide.fa +24 -0
  72. data/data/raw_data/Protostomian_CCH_amide.fa.aligned.fa +72 -0
  73. data/data/raw_data/Protostomian_Ecdysis_Triggering_Hormone.fa +24 -0
  74. data/data/raw_data/Protostomian_Ecdysis_Triggering_Hormone.fa.aligned.fa +84 -0
  75. data/data/raw_data/Protostomian_PDF.fa +16 -0
  76. data/data/raw_data/Protostomian_PDF.fa.aligned.fa +32 -0
  77. data/data/raw_data/Protostomian_allatostatin_C.fa +28 -0
  78. data/data/raw_data/Protostomian_allatostatin_C.fa.aligned.fa +56 -0
  79. data/data/raw_data/Protostomian_proctolin.fa +16 -0
  80. data/data/raw_data/Protostomian_proctolin.fa.aligned.fa +32 -0
  81. data/data/raw_data/Putative_chordate_Opioid.fa +8 -0
  82. data/data/raw_data/Putative_chordate_Opioid.fa.aligned.fa +32 -0
  83. data/data/raw_data/SIF.fa +28 -0
  84. data/data/raw_data/SIF.fa.aligned.fa +70 -0
  85. data/data/raw_data/TRH.fa +10 -0
  86. data/data/raw_data/TRH.fa.aligned.fa +50 -0
  87. data/data/raw_data/allatotropin.fa +31 -0
  88. data/data/raw_data/allatotropin.fa.aligned.fa +90 -0
  89. data/data/raw_data/ambulacrarian_amphioxus_NPS-like.fa +8 -0
  90. data/data/raw_data/ambulacrarian_amphioxus_NPS-like.fa.aligned.fa +24 -0
  91. data/data/raw_data/avp.fa +28 -0
  92. data/data/raw_data/avp.fa.aligned.fa +70 -0
  93. data/data/raw_data/calcitonin_DH31.fa +36 -0
  94. data/data/raw_data/calcitonin_DH31.fa.aligned.fa +126 -0
  95. data/data/raw_data/cholecystokinin_sulfakinin.fa +28 -0
  96. data/data/raw_data/cholecystokinin_sulfakinin.fa.aligned.fa +84 -0
  97. data/data/raw_data/chordate_OX26_QRFP.fa +10 -0
  98. data/data/raw_data/chordate_OX26_QRFP.fa.aligned.fa +25 -0
  99. data/data/raw_data/chordate_somatostatin_cortistatin_like.fa +10 -0
  100. data/data/raw_data/chordate_somatostatin_cortistatin_like.fa.aligned.fa +20 -0
  101. data/data/raw_data/f_type_SALMF.fa +118 -0
  102. data/data/raw_data/f_type_SALMF.fa.aligned.fa +590 -0
  103. data/data/raw_data/galanin.fa +93 -0
  104. data/data/raw_data/galanin.fa.aligned.fa +552 -0
  105. data/data/raw_data/kisspeptin.fa +16 -0
  106. data/data/raw_data/kisspeptin.fa.aligned.fa +0 -0
  107. data/data/raw_data/l_type_SALMF.fa +68 -0
  108. data/data/raw_data/l_type_SALMF.fa.aligned.fa +170 -0
  109. data/data/raw_data/nmu_pyrokinin.fa +18 -0
  110. data/data/raw_data/nmu_pyrokinin.fa.aligned.fa +63 -0
  111. data/data/raw_data/npy_npf.fa +20 -0
  112. data/data/raw_data/npy_npf.fa.aligned.fa +40 -0
  113. data/data/raw_data/protostomian_CCAP.fa +14 -0
  114. data/data/raw_data/protostomian_CCAP.fa.aligned.fa +42 -0
  115. data/data/raw_data/protostomian_allatostatinA_buccalin.fa +100 -0
  116. data/data/raw_data/protostomian_allatostatinA_buccalin.fa.aligned.fa +1350 -0
  117. data/data/raw_data/protostomian_leucokinin.fa +18 -0
  118. data/data/raw_data/protostomian_leucokinin.fa.aligned.fa +63 -0
  119. data/data/raw_data/protostomian_tackykinin.fa +504 -0
  120. data/data/raw_data/protostomian_tackykinin.fa.aligned.fa +2002 -0
  121. data/data/raw_data/tachykinin.fa.aligned.fa +13546 -0
  122. data/data/raw_data/vertebrate_ghrelin_motilin.fa +16 -0
  123. data/data/raw_data/vertebrate_ghrelin_motilin.fa.aligned.fa +32 -0
  124. data/lib/neurohmmer.rb +89 -0
  125. data/lib/neurohmmer/arg_validators.rb +71 -0
  126. data/lib/neurohmmer/hmmer.rb +71 -0
  127. data/lib/neurohmmer/output.rb +50 -0
  128. data/lib/neurohmmer/version.rb +4 -0
  129. data/neurohmmer.gemspec +34 -0
  130. data/spec/neurohmmer_spec.rb +11 -0
  131. data/spec/spec_helper.rb +2 -0
  132. data/template/contents.slim +55 -0
  133. metadata +269 -0
data/data/hmm/Protostomian_CCH_amide.fa.hmm ADDED
@@ -0,0 +1,415 @@
1
+ HMMER3/f [3.1b2 | February 2015]
2
+ NAME Protostomian_CCH_amide.fa.aligned
3
+ LENG 131
4
+ ALPH amino
5
+ RF no
6
+ MM no
7
+ CONS yes
8
+ CS no
9
+ MAP yes
10
+ DATE Fri Sep 18 18:52:06 2015
11
+ NSEQ 12
12
+ EFFN 2.305664
13
+ CKSUM 2107830234
14
+ STATS LOCAL MSV -9.9182 0.71178
15
+ STATS LOCAL VITERBI -11.4448 0.71178
16
+ STATS LOCAL FORWARD -3.7227 0.71178
17
+ HMM A C D E F G H I K L M N P Q R S T V W Y
18
+ m->m m->i m->d i->m i->i d->m d->d
19
+ COMPO 2.60444 3.83663 2.95308 2.64692 3.50952 2.75016 3.52617 3.13651 2.62522 2.63730 3.58779 2.82461 3.23361 2.94232 2.81148 2.52086 2.87925 2.83319 4.62312 3.63808
20
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
21
+ 0.01324 4.72722 5.44956 0.61958 0.77255 0.00000 *
22
+ 1 3.93619 5.37733 5.15170 4.89447 3.96027 4.60722 5.43562 3.24934 4.62021 2.48641 0.36428 5.04598 5.13363 4.96738 4.70663 4.33252 4.29266 3.34485 5.84704 4.67296 1 M - - -
23
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+ 0.05850 4.72722 3.03722 0.61958 0.77255 0.48576 0.95510
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+ 2 2.21793 5.15472 3.07018 2.18347 4.45517 3.56008 2.68723 3.90726 2.04911 3.02899 4.20837 2.76605 3.95152 2.86162 2.66632 2.75597 2.99887 3.52148 3.22399 4.23612 2 k - - -
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+ 0.09193 4.68256 2.54364 0.61958 0.77255 0.57537 0.82667
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+ 3 2.73133 3.44648 3.93232 3.35543 3.40668 3.78545 4.06796 1.94570 3.27196 2.28907 3.40433 2.66013 4.15913 2.87703 3.53454 2.71474 2.96336 2.34027 4.89474 2.69626 3 i - - -
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+ 0.21296 4.60559 1.70478 0.61958 0.77255 0.70556 0.68088
31
+ 4 2.66813 4.49969 3.39222 2.82778 3.65646 3.60268 3.84096 3.02745 2.78576 2.37268 3.59847 2.78857 3.22596 3.11225 2.80725 2.83607 2.04943 2.51289 3.69940 3.81089 4 t - - -
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+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
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+ 0.01821 4.41084 5.13319 0.61958 0.77255 0.38908 1.13221
34
+ 5 2.17789 3.46282 3.65991 3.11162 3.14992 3.62254 4.07768 3.19424 3.06271 2.89943 3.77933 3.48836 4.09672 3.37639 2.91932 1.30424 3.01003 2.92887 5.24632 4.00448 5 s - - -
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+ 0.01406 4.66712 5.38947 0.61958 0.77255 0.60372 0.79136
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+ 6 2.76270 4.94081 3.17864 2.62978 4.20397 3.10671 3.81438 3.61703 2.18587 3.22437 4.04057 3.14161 3.98917 2.68023 3.05925 2.33313 1.85241 2.44762 5.47017 4.14217 6 t - - -
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+ 0.01406 4.66712 5.38947 0.61958 0.77255 0.60372 0.79136
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+ 7 2.75454 2.90507 3.94523 3.36912 2.94636 3.80552 4.09011 1.99189 3.28814 2.52332 3.43394 2.54878 4.18064 3.06816 3.55438 2.43843 2.68358 2.36038 4.92467 3.71786 7 i - - -
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+ 0.01202 4.42678 * 0.61958 0.77255 0.00000 *
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+ //
data/data/hmm/Protostomian_Ecdysis_Triggering_Hormone.fa.hmm ADDED
@@ -0,0 +1,433 @@
1
+ HMMER3/f [3.1b2 | February 2015]
2
+ NAME Protostomian_Ecdysis_Triggering_Hormone.fa.aligned
3
+ LENG 137
4
+ ALPH amino
5
+ RF no
6
+ MM no
7
+ CONS yes
8
+ CS no
9
+ MAP yes
10
+ DATE Fri Sep 18 18:52:06 2015
11
+ NSEQ 12
12
+ EFFN 2.610352
13
+ CKSUM 102432536
14
+ STATS LOCAL MSV -10.0524 0.71095
15
+ STATS LOCAL VITERBI -11.4220 0.71095
16
+ STATS LOCAL FORWARD -4.1534 0.71095
17
+ HMM A C D E F G H I K L M N P Q R S T V W Y
18
+ m->m m->i m->d i->m i->i d->m d->d
19
+ COMPO 2.64108 4.51586 2.83570 2.67198 3.32664 2.95477 3.79794 2.96743 2.56993 2.52997 3.62496 2.92753 3.01166 3.07470 2.71043 2.53707 2.88495 2.86158 4.52326 3.61783
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433
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