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_CCAP.fa.hmm ADDED
@@ -0,0 +1,415 @@
1
+ HMMER3/f [3.1b2 | February 2015]
2
+ NAME protostomian_CCAP.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 7
12
+ EFFN 1.493652
13
+ CKSUM 90246755
14
+ STATS LOCAL MSV -9.8586 0.71180
15
+ STATS LOCAL VITERBI -11.3774 0.71180
16
+ STATS LOCAL FORWARD -4.1149 0.71180
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 2.61365 3.65370 3.05409 2.67402 3.32933 2.84961 3.80718 3.03871 2.53900 2.50923 3.68084 2.86258 3.28094 3.01751 2.74922 2.51869 2.87330 2.82921 4.93975 3.70822
20
+ 2.68628 4.42235 2.77530 2.73134 3.46364 2.40523 3.72505 3.29364 2.67751 2.69365 4.24394 2.90357 2.73750 3.18157 2.89811 2.37878 2.77489 2.98493 4.58487 3.61513
21
+ 0.23082 1.60782 5.15044 0.81940 0.58106 0.00000 *
22
+ 1 3.49674 4.85334 4.99445 4.48796 2.37613 4.61604 4.74246 2.54971 4.32527 1.72412 0.97147 4.65090 4.87194 4.42813 4.42015 3.99259 3.73486 2.68575 5.00724 3.65713 4 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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+ 0.01789 4.42809 5.15044 0.61958 0.77255 0.48576 0.95510
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+ 2 2.68548 4.66666 3.25010 2.68687 3.85466 3.56877 3.78398 2.61342 2.63636 2.89928 2.84084 2.74404 3.95451 2.59189 2.52963 2.79009 2.21653 2.96843 5.20650 3.92289 5 t - - -
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+ 0.01789 4.42809 5.15044 0.61958 0.77255 0.48576 0.95510
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+ 3 2.68691 3.18972 3.10799 2.54913 4.10831 3.51674 2.83893 3.52080 2.50910 3.12787 3.94564 3.06137 3.91022 2.51955 2.56882 2.14878 2.45560 3.20175 5.37385 4.04829 6 s - - -
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+ 4 2.70708 4.84401 3.06534 2.71598 4.47644 3.39533 3.97566 3.93073 2.77655 3.51680 4.33279 3.17483 2.83631 2.54456 3.19116 1.16833 3.04766 3.50447 5.71261 4.38692 7 s - - -
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+ 0.01789 4.42809 5.15044 0.61958 0.77255 0.48576 0.95510
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+ 5 2.67406 4.12069 4.25088 3.65892 2.68189 3.79421 2.90459 2.55729 3.51922 2.05165 2.57715 3.81873 4.16115 3.71950 3.66096 3.08692 2.36530 2.06271 3.38498 3.52749 8 l - - -
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+ 0.01789 4.42809 5.15044 0.61958 0.77255 0.48576 0.95510
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+ 6 2.34856 4.29686 3.74857 3.17645 2.33528 3.70083 3.97668 2.75737 3.10109 2.15509 3.39990 3.52363 2.90443 3.38559 2.68129 2.96307 2.91150 2.28139 4.89296 3.67560 9 l - - -
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+ 7 2.67817 4.48829 3.42581 2.86665 3.62294 3.61618 2.87348 2.49020 2.82497 2.71137 3.59334 3.30362 4.00335 3.14773 3.20647 2.07884 2.26991 2.77460 5.04552 3.02106 10 s - - -
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411
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412
+ 131 2.66906 4.81470 3.07593 2.52366 4.02458 3.48704 3.66733 3.45563 2.06614 2.45981 3.89043 2.60777 3.87675 2.44112 2.81611 2.71304 2.89532 3.14761 5.28951 3.05353 263 k - - -
413
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414
+ 0.01523 4.19179 * 0.61958 0.77255 0.00000 *
415
+ //
data/data/hmm/protostomian_allatostatinA_buccalin.fa.hmm ADDED
@@ -0,0 +1,706 @@
1
+ HMMER3/f [3.1b2 | February 2015]
2
+ NAME protostomian_allatostatinA_buccalin.fa.aligned
3
+ LENG 228
4
+ ALPH amino
5
+ RF no
6
+ MM no
7
+ CONS yes
8
+ CS no
9
+ MAP yes
10
+ DATE Fri Sep 18 18:52:05 2015
11
+ NSEQ 50
12
+ EFFN 2.517700
13
+ CKSUM 3310955750
14
+ STATS LOCAL MSV -11.3048 0.70386
15
+ STATS LOCAL VITERBI -13.3578 0.70386
16
+ STATS LOCAL FORWARD -4.4842 0.70386
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 2.63698 4.55719 2.84690 2.71734 3.27956 2.46528 3.77799 3.28194 2.51138 2.61411 3.91922 3.01289 3.12491 3.10082 2.69138 2.50515 2.89038 3.00916 4.82570 3.32156
20
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21
+ 1.19167 0.94783 1.17537 3.43163 0.03287 0.00000 *
22
+ 1 2.20798 4.89233 3.02458 2.51643 4.13500 3.50847 2.84641 3.55314 2.19552 3.15160 3.03575 3.03624 3.89804 2.79138 2.63067 2.54540 2.91206 3.22696 5.39013 3.22425 127 k - - -
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27
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701
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705
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706
+ //