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/Deutrostomian_tachykinin.fa.hmm ADDED
@@ -0,0 +1,367 @@
1
+ HMMER3/f [3.1b2 | February 2015]
2
+ NAME Deutrostomian_tachykinin.fa.aligned
3
+ LENG 115
4
+ ALPH amino
5
+ RF no
6
+ MM no
7
+ CONS yes
8
+ CS no
9
+ MAP yes
10
+ DATE Fri Sep 18 18:51:57 2015
11
+ NSEQ 439
12
+ EFFN 1.389961
13
+ CKSUM 3517185177
14
+ STATS LOCAL MSV -9.7008 0.71440
15
+ STATS LOCAL VITERBI -10.7349 0.71440
16
+ STATS LOCAL FORWARD -4.1794 0.71440
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 2.61500 4.63696 2.89770 2.63558 3.24177 2.83792 3.68774 3.04472 2.55488 2.49900 3.49419 3.07478 3.33252 2.94510 2.71961 2.59846 2.93364 2.83594 4.20785 3.56618
20
+ 2.68480 4.42237 2.77679 2.73122 3.46425 2.40535 3.72422 3.29403 2.67805 2.69350 4.24169 2.90435 2.73691 3.18208 2.89813 2.37923 2.77596 2.98072 4.58592 3.61751
21
+ 0.19837 1.84211 3.84179 4.08666 0.01694 0.00000 *
22
+ 1 3.42110 4.84549 4.78041 4.30018 3.27900 4.47577 4.86583 2.46222 4.01197 1.64632 0.93536 4.54031 4.79985 4.30651 4.16031 3.89602 3.68677 2.56204 5.29068 4.09481 175 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
24
+ 0.03235 4.35637 3.96269 0.61958 0.77255 0.50849 0.91980
25
+ 2 2.89277 5.25208 3.05384 2.46945 4.63417 3.59360 3.69007 4.05292 1.30010 3.51695 4.31144 3.02450 3.98397 2.70171 2.15245 2.60039 3.09994 3.66894 5.61434 4.30963 176 k - - -
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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
27
+ 0.01949 4.34350 5.06585 0.61958 0.77255 0.50199 0.92970
28
+ 3 2.77934 4.22367 4.28619 3.70679 3.26000 3.92197 4.25023 1.32227 3.57787 2.13557 3.19118 3.91427 4.27915 3.55171 3.74346 2.98907 2.92847 1.98667 4.90940 3.71948 177 i - - -
29
+ 2.68626 4.42235 2.77532 2.73097 3.46376 2.40520 3.72457 3.29366 2.67754 2.69364 4.24712 2.90365 2.73726 3.18112 2.89776 2.37888 2.77526 2.98521 4.58431 3.61490
30
+ 0.16039 1.95229 5.07638 1.74590 0.19175 0.49406 0.94198
31
+ 4 2.66338 4.15695 3.80801 3.23437 3.34879 3.69720 3.99062 2.67329 2.96334 1.38037 3.32899 3.55663 3.53728 3.41999 3.34315 2.80741 2.90344 2.38180 4.86936 3.65981 207 l - - -
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
+ 0.01914 4.36149 5.08383 0.61958 0.77255 0.50104 0.93115
34
+ 5 2.83938 3.94415 4.42050 3.43621 3.01307 4.01076 4.35219 2.25218 3.71488 1.82765 3.30042 4.02938 4.36030 3.92890 3.87596 3.31661 3.07663 1.24693 4.96780 3.77495 208 v - - -
35
+ 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
36
+ 0.02285 4.36149 4.62187 0.61958 0.77255 0.50104 0.93115
37
+ 6 1.65138 4.58329 3.27724 2.72057 3.77546 3.54889 3.58494 3.14178 2.67716 2.65794 3.69178 3.18796 3.68171 2.88682 2.92071 2.61139 2.89204 2.57053 5.14875 3.87578 209 a - - -
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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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+ 0.01921 4.35784 5.08019 0.61958 0.77255 0.50636 0.92303
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+ 7 2.64497 4.04776 4.34903 3.76210 2.70231 3.77511 4.21301 2.41248 3.61957 1.28699 3.20582 3.92408 4.24714 3.81665 3.61988 3.17944 2.98304 2.05712 4.81365 3.62922 210 l - - -
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+ 0.01920 4.35809 5.08044 0.61958 0.77255 0.50636 0.92303
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+ 8 1.59403 3.90757 3.69632 3.21919 3.20249 3.68317 3.99499 2.67323 3.14518 2.22902 3.38131 3.54611 4.07295 3.41982 3.27111 2.95546 2.79774 2.19369 4.88369 3.67122 211 a - - -
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+ 0.02146 4.35809 4.77641 0.61958 0.77255 0.49759 0.93647
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+ 9 3.17164 4.50608 4.96982 4.28843 3.64687 4.57252 5.03668 1.77687 4.31486 1.94050 3.25801 4.62771 4.85146 4.53940 4.48005 3.92722 3.45089 0.88918 5.53276 4.35445 212 v - - -
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+ 0.14801 2.31197 3.25687 2.56144 0.08034 0.50426 0.92622
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+ 10 2.79239 4.28008 4.58970 4.00191 2.11075 4.06816 4.38305 2.06598 3.85130 1.37416 3.10402 4.13397 4.39348 4.00791 3.95232 3.18757 3.12243 2.14656 4.88943 3.71537 256 l - - -
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+ 11 2.91633 4.03911 4.60973 4.03106 1.52390 4.11449 4.41961 2.38067 3.88472 1.56719 3.12922 4.17368 4.44380 4.04462 3.99832 3.43071 3.02749 2.18015 4.91279 3.70096 258 f - - -
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+ 12 2.70866 4.22999 4.02085 3.45722 3.32227 3.65523 4.13512 2.51854 3.34400 1.26775 3.32647 3.72012 4.16225 3.61056 3.58159 2.64980 2.78309 2.30816 4.92030 3.71910 259 l - - -
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+ 13 2.12116 4.14351 4.11349 3.41509 2.85979 3.77228 4.08010 2.24584 3.41360 2.22745 3.20276 3.74642 4.14110 3.63872 3.60252 2.75219 2.82840 1.73129 4.77249 3.53506 260 v - - -
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+ //
data/data/hmm/Gastrin_releasing_peptide.fa.hmm ADDED
@@ -0,0 +1,448 @@
1
+ HMMER3/f [3.1b2 | February 2015]
2
+ NAME Gastrin_releasing_peptide.fa.aligned
3
+ LENG 142
4
+ ALPH amino
5
+ RF no
6
+ MM no
7
+ CONS yes
8
+ CS no
9
+ MAP yes
10
+ DATE Fri Sep 18 18:51:59 2015
11
+ NSEQ 5
12
+ EFFN 1.264648
13
+ CKSUM 3368578004
14
+ STATS LOCAL MSV -9.9599 0.71035
15
+ STATS LOCAL VITERBI -11.2446 0.71035
16
+ STATS LOCAL FORWARD -4.0536 0.71035
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 2.59806 4.58581 2.92890 2.60825 3.55362 2.81565 3.62576 3.07588 2.54564 2.47667 3.55444 2.97216 3.26955 2.93956 2.77918 2.56513 2.93070 2.73896 4.40722 3.70214
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21
+ 0.01986 4.32458 5.04693 0.61958 0.77255 0.00000 *
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+ //