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/PTH.fa.hmm ADDED
@@ -0,0 +1,502 @@
1
+ HMMER3/f [3.1b2 | February 2015]
2
+ NAME PTH.fa.aligned
3
+ LENG 160
4
+ ALPH amino
5
+ RF no
6
+ MM no
7
+ CONS yes
8
+ CS no
9
+ MAP yes
10
+ DATE Fri Sep 18 18:52:10 2015
11
+ NSEQ 12
12
+ EFFN 2.809570
13
+ CKSUM 3745831403
14
+ STATS LOCAL MSV -10.0188 0.70841
15
+ STATS LOCAL VITERBI -11.4030 0.70841
16
+ STATS LOCAL FORWARD -4.3220 0.70841
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 2.57177 4.54727 2.89502 2.62742 3.56612 2.73856 3.65300 3.13445 2.59349 2.49165 3.64244 3.05916 3.19790 3.02560 2.68367 2.49903 2.75515 2.86484 4.66545 3.79123
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
+ 0.05370 4.87601 3.10875 0.61958 0.77255 0.00000 *
22
+ 1 4.10155 5.52973 5.31483 5.08503 4.11376 4.72689 5.60510 3.42324 4.81355 2.63949 0.29973 5.22127 5.26645 5.15603 4.88313 4.49738 4.46767 3.52850 5.99143 4.82897 1 M - - -
23
+ 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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+ 0.44090 4.83420 1.05386 0.61958 0.77255 0.58290 0.81707
25
+ 2 1.93768 4.79748 3.12735 2.27885 4.02540 3.52031 3.73533 3.02466 2.54824 3.05307 3.88279 3.07869 3.02117 2.90363 2.48326 2.73359 2.90926 2.81473 5.32195 4.00632 2 a - - -
26
+ 2.68616 4.42054 2.77556 2.73160 3.46391 2.40550 3.72353 3.29359 2.67778 2.69323 4.24552 2.90362 2.73758 3.18136 2.89763 2.37911 2.77441 2.98555 4.58514 3.61443
27
+ 0.73924 0.66043 5.13384 1.11410 0.39781 0.50444 0.92595
28
+ 3 2.54056 2.49017 4.04854 3.47331 3.44857 3.27501 4.14680 2.78729 3.38056 1.90071 3.44810 3.74880 4.21334 3.07302 3.62415 3.10607 1.97655 2.28274 4.94191 3.74022 7 l - - -
29
+ 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
30
+ 0.01345 4.71141 5.43376 0.61958 0.77255 0.80643 0.59140
31
+ 4 2.80110 5.15589 3.10476 2.55280 4.45452 3.58813 3.77619 3.90014 2.34547 3.43913 4.21804 2.81527 2.32635 2.89581 2.31014 1.88233 3.03121 3.52423 5.61818 3.21625 8 s - - -
32
+ 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
33
+ 0.01345 4.71141 5.43376 0.61958 0.77255 0.43578 1.04060
34
+ 5 3.05206 5.13580 3.04072 2.91128 4.38408 3.83609 3.96090 3.76612 2.16063 1.29168 4.21173 3.38566 4.22067 3.12643 1.96527 3.10303 3.26535 3.47678 5.59164 4.32309 9 l - - -
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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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+ 0.01189 4.83420 5.55654 0.61958 0.77255 0.42948 1.05224
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+ 6 2.13612 4.29897 4.47129 3.87837 3.39889 3.98620 4.30394 2.29946 3.73447 2.00166 1.89076 4.02580 2.97302 3.93036 3.86667 2.77489 3.09267 2.18961 4.92070 3.73506 10 m - - -
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+ 0.01140 4.87601 5.59836 0.61958 0.77255 0.48576 0.95510
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+ 7 2.31218 4.44514 3.95252 3.37944 3.56832 2.94268 4.15648 2.64076 2.97712 2.12522 3.55761 3.71486 2.59496 3.58185 3.59894 3.13986 2.54327 1.80141 5.04684 3.83415 11 v - - -
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+ 8 2.45177 5.30291 3.13643 2.24953 4.63074 3.63862 3.81523 4.09396 2.37431 3.59395 2.45738 2.68607 4.03008 2.32561 1.89618 2.83659 3.09093 3.68487 5.73962 4.35533 12 r - - -
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