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/calcitonin_DH31.fa.hmm ADDED
@@ -0,0 +1,418 @@
1
+ HMMER3/f [3.1b2 | February 2015]
2
+ NAME calcitonin_DH31.fa.aligned
3
+ LENG 132
4
+ ALPH amino
5
+ RF no
6
+ MM no
7
+ CONS yes
8
+ CS no
9
+ MAP yes
10
+ DATE Fri Sep 18 18:51:49 2015
11
+ NSEQ 18
12
+ EFFN 3.722168
13
+ CKSUM 3067038969
14
+ STATS LOCAL MSV -9.7147 0.71165
15
+ STATS LOCAL VITERBI -11.3032 0.71165
16
+ STATS LOCAL FORWARD -3.9786 0.71165
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 2.54024 3.84133 2.98012 2.71540 3.50068 2.79900 3.74141 3.14669 2.67393 2.41791 3.50205 2.99788 3.31584 2.98162 2.64266 2.52979 2.79930 2.86698 5.02346 3.70189
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
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+ 0.00910 5.09946 5.82181 0.61958 0.77255 0.00000 *
22
+ 1 4.54197 5.93400 5.72699 5.56539 4.54467 5.03873 6.04185 3.91202 5.31681 3.07910 0.18054 5.67117 5.61012 5.64539 5.34409 4.93104 4.93231 4.03812 6.37834 5.25340 1 M - - -
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+ 0.00910 5.09946 5.82181 0.61958 0.77255 0.48576 0.95510
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+ 2 2.59532 4.83520 3.13552 3.01454 4.00329 2.46839 4.07654 2.56194 2.33610 2.80481 3.31335 3.48133 4.23095 3.31740 2.90594 2.53637 2.90061 2.10471 5.39097 3.28761 2 v - - -
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+ 2.68692 4.42320 2.77615 2.73110 3.46270 2.40576 3.72590 3.29246 2.67794 2.69309 4.24593 2.90420 2.73665 3.18106 2.89809 2.37819 2.77430 2.98487 4.58572 3.61599
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+ 1.16610 0.73630 1.56284 1.45046 0.26718 0.48576 0.95510
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+ 3 2.83561 3.34330 3.74452 3.17611 2.81752 3.82301 4.07921 3.03118 3.12634 2.17366 2.48689 2.56807 4.20177 2.86723 2.49034 2.75295 2.64199 2.80909 5.12174 3.89096 20 l - - -
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+ 0.11404 4.86807 2.30173 0.61958 0.77255 0.68174 0.70468
31
+ 4 2.47456 2.99954 4.00306 3.42720 2.59428 3.88194 4.16165 2.87568 3.34898 2.38669 3.08205 2.49589 4.25608 3.61330 3.14132 2.18767 3.06639 2.66997 5.00882 2.60946 21 s - - -
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+ 0.01159 4.85904 5.58139 0.61958 0.77255 0.99596 0.46103
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+ 5 1.82697 4.33078 4.25723 3.67289 3.01586 3.93343 4.23793 2.50852 3.56085 2.14637 3.44706 3.89859 3.00014 3.78855 3.75712 2.76336 2.23942 2.05134 4.94491 3.75080 22 a - - -
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+ 0.01159 4.85904 5.58139 0.61958 0.77255 0.55588 0.85230
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+ 6 2.92584 3.55157 4.84222 4.23217 2.06010 4.09502 4.42987 2.40844 4.02968 1.64090 3.41988 4.24161 4.45764 4.17073 4.05659 2.88911 2.36804 1.79260 4.93638 3.75931 23 l - - -
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+ 0.01017 4.98908 5.71143 0.61958 0.77255 0.76755 0.62389
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+ 7 2.61734 2.40305 4.68651 4.08304 3.03251 3.16160 4.37457 2.74113 3.90582 1.97707 2.23715 3.45290 4.41548 4.07035 3.97703 2.86517 3.13357 1.79277 4.92556 3.74508 24 v - - -
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+ 8 2.13295 3.50604 3.44337 2.88548 4.17848 3.75549 4.01603 3.57282 2.56669 3.22045 4.06181 3.37199 4.16339 3.20713 2.69852 1.44650 2.62199 2.80697 5.50935 4.21209 25 s - - -
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+ 0.01009 4.60101 * 0.61958 0.77255 0.00000 *
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+ //
data/data/hmm/cholecystokinin_sulfakinin.fa.hmm ADDED
@@ -0,0 +1,433 @@
1
+ HMMER3/f [3.1b2 | February 2015]
2
+ NAME cholecystokinin_sulfakinin.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 18:51:49 2015
11
+ NSEQ 14
12
+ EFFN 2.478027
13
+ CKSUM 1869694653
14
+ STATS LOCAL MSV -10.0622 0.71097
15
+ STATS LOCAL VITERBI -11.4479 0.71097
16
+ STATS LOCAL FORWARD -3.4299 0.71097
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 2.62074 4.58709 2.79735 2.66123 3.33139 2.69249 3.61136 3.21573 2.50754 2.65810 3.56657 3.03747 3.29685 3.00617 2.70821 2.54057 2.89324 2.89281 4.41014 3.41269
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432
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433
+ //