neurohmmer 0.1.0

data/README.md

@@ -0,0 +1,136 @@
+# NeuroHMMer - Identify homologs to known Neuropeptides
+
+## Coming Soon. Alpha - Things may break...
+
+This is a program that will utilise the power of Hidden Markov Model profiles to identify homologs to known neuropeptides. Neurohmmer uses 37 separate, precalculated models for each neuropeptide group. This allows for quick and accurate analysis of existing and newly sequenced transcriptomic or proteomic data. A typical analysis of a fasta file with 30,000 sequences takes under 5 minutes on an average machine.
+
+If you use NeuroHMMer in your work, please cite us as follows:
+
+> "Moghul I, Elphick MR, Wurm Y (<em>in prep.</em>) NeuroHMMer: identify homolgos to known neuropeptides"
+
+### Neuropeptides Homologs
+
+NeuroHmmer currently uses Hidden Markov Models for the following neuropeptides (in alphabetic order):
+
+* Allatotropin
+* Ambulacrarian/ Amphioxus NPS-like
+* AVP
+* Calcitonin/ DH31
+* Cholecystokinin/ Sulfakinin
+* Chordate Glucagon PACAP
+* Chordate Neurotensin precursors neurotensin like Ciona
+* Chordate OX26 QRFP
+* Chordate somatostatin cortistatin like
+* CRH/DH44
+* Deutrostomian Tachykinin
+* F-type SALMFamide
+* Galanin
+* Gastrin releasing peptide
+* GnRH
+* Hypocretin orexin
+* L-type SALMFamide
+* Lophotrochozoan luqin arthropod RYamide
+* NMi pyrokinin
+* NPFF
+* NPS
+* NPY / NPF
+* Protostomian Allatostatin A / Buccalin
+* Protostomian Allatostatin B
+* Protostomian Allatostatin C
+* Protostomian CCAP
+* Protostomian CCH-amide
+* Protostomian Ecdysis Triggering Hormone
+* Protostomian Leucokinin
+* Protostomian PDF
+* Protostomian Proctolin
+* Protostomian Tackykinin
+* PTH
+* Putative Chordate Opioid
+* SIF
+* TRH
+* Vertebrate Ghrelin Motilin
+
+## Installation
+### Installation Requirements
+* Ruby (>= 2.0.0)
+* HMMer (>=3.0)
+
+### Installation
+Simply run the following command in the terminal.
+
+```bash
+gem install neurohmmer
+```
+
+If that doesn't work, try `sudo gem install neurohmmer` instead.
+
+##### Running From Source (Not Recommended)
+It is also possible to run from source. However, this is not recommended.
+
+```bash
+# Clone the repository.
+git clone https://github.com/wurmlab/neurohmmer.git
+
+# Move into NeuroHmmer source directory.
+cd neurohmmer
+
+# Install bundler
+gem install bundler
+
+# Use bundler to install dependencies
+bundle install
+
+# Optional: run tests, build documentation and build the gem from source
+bundle exec rake
+
+# Run NeuroHMMer.
+bundle exec neurohmmer -h
+# note that `bundle exec` executes NeuroHMMer in the context of the bundle
+
+# Alternativaly, install NeuroHMMer as a gem
+bundle exec rake install
+neurohmmer -h
+```
+
+## Usage
+Verify NeuroHMMer installed by running the following command in the terminal:
+
+```bash
+neurohmmer
+```
+
+You should see the following output.
+
+```bash
+
+DESCRIPTION:
+Neurohmmer is a tool that identifies neuropeptide homologs by using the power
+of Hidden Markov Models. Neurohmmer uses .. separate, precalculated models for
+each neuropeptide group.
+
+USAGE:
+    neurohmmer [OPTIONS] Input_File
+
+ARGUMENTS:
+
+
+OPTIONAL ARGUMENTS
+    -d, --temp_dir path_to_temp_dir  The full path to the temp directory. Neurohmmer creates this
+                                      directory if it does already exist and then delete the directory
+                                      once it has finished using them.
+                                      Default: Hidden folder in the current working dirctory
+    -n, --num_threads num_of_threads The number of threads to use when analysing the input file
+        --version                    The version of Neurohmmer that you are running.
+    -h, --help                       Show this screen.
+
+```
+
+
+
+
+
+
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/wurmlab/neurohmmer. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](contributor-covenant.org) code of conduct.

data/Rakefile

@@ -0,0 +1,17 @@
+require 'bundler/gem_tasks'
+require 'rspec/core/rake_task'
+
+task default: :build
+
+desc 'Builds and installs'
+task install: [:build] do
+  require_relative 'lib/neurohmmer/version'
+  sh "gem install ./neurohmmer-#{Neurohmmer::VERSION}.gem"
+end
+
+desc 'Runs tests, generates documentation, builds gem (default)'
+task build: [:test] do
+  sh 'gem build neurohmmer.gemspec'
+end
+
+RSpec::Core::RakeTask.new(:spec)

data/bin/neurohmmer

@@ -0,0 +1,69 @@
+#!/usr/bin/env ruby
+require 'optparse'
+
+require 'neurohmmer'
+require 'neurohmmer/version'
+
+opt = {}
+optparse = OptionParser.new do |opts|
+  opts.banner = <<BANNER
+
+DESCRIPTION:
+Neurohmmer is a tool that identifies neuropeptide homologs by using the power
+of Hidden Markov Models. Neurohmmer uses .. separate, precalculated models for
+each neuropeptide group.
+
+USAGE:
+    neurohmmer [OPTIONS] Input_File
+
+ARGUMENTS:
+
+
+OPTIONAL ARGUMENTS
+BANNER
+  opt[:temp_dir] = File.join(Dir.pwd, '.temp')
+  opts.on('-d', '--temp_dir path_to_temp_dir',
+          'The full path to the temp directory. Neurohmmer creates this',
+          ' directory if it does already exist and then delete the directory',
+          ' once it has finished using them.',
+          ' Default: Hidden folder in the current working dirctory') do |p|
+    opt[:temp_dir] = p
+  end
+
+  opt[:num_threads] = 1
+  opts.on('-n', '--num_threads num_of_threads', Integer,
+          'The number of threads to use when analysing the input file') do |n|
+    opt[:num_threads] = n
+  end
+
+  opts.on('--version', 'The version of Neurohmmer that you are running.') do
+    puts Neurohmmer::VERSION
+    exit
+  end
+
+  opts.on('-h', '--help', 'Show this screen.') do
+    $stderr.puts optparse
+    exit
+  end
+end
+
+begin
+  optparse.parse!
+  if ARGV.length > 1
+    $stderr.puts "Error: It seems that you have #{ARGV.length} input fasta" \
+                 ' files. Please ensure that you have a single input fasta' \
+                 " file\n"
+    exit 1
+  elsif ARGV.length == 0
+    $stderr.puts optparse
+    exit 1
+  end
+rescue OptionParser::ParseError
+  $stderr.print 'Error: ' + $ERROR_INFO.to_s + '\n'
+  exit 1
+end
+
+opt[:input_file] = ARGV[0]
+
+Neurohmmer.init(opt)
+Neurohmmer.run

data/data/hmm/CRH_DH44.fa.hmm

@@ -0,0 +1,427 @@
+HMMER3/f [3.1b2 | February 2015]
+NAME  CRH_DH44.fa.aligned
+LENG  135
+ALPH  amino
+RF    no
+MM    no
+CONS  yes
+CS    no
+MAP   yes
+DATE  Fri Sep 18 18:51:51 2015
+NSEQ  22
+EFFN  4.605713
+CKSUM 243285233
+STATS LOCAL MSV       -9.8760  0.71122
+STATS LOCAL VITERBI  -11.2300  0.71122
+STATS LOCAL FORWARD   -3.6591  0.71122
+HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   2.59238  4.42844  2.90605  2.66970  3.64653  2.73221  3.76437  3.13176  2.62726  2.43011  3.69308  2.98081  3.03113  3.03128  2.68585  2.44447  2.88135  2.87030  4.74604  3.79634
+          2.68631  4.42238  2.77532  2.73136  3.46367  2.40526  3.72507  3.29367  2.67754  2.69368  4.23799  2.90359  2.73752  3.18159  2.89814  2.37900  2.77532  2.98531  4.58490  3.61516
+          0.29425  1.37698  5.96402  0.08765  2.47796  0.00000        *
+      1   4.35323  5.61701  6.17609  5.70519  3.89976  5.60288  6.09517  2.39747  5.44938  2.18572  0.41749  5.86392  5.78107  5.48950  5.45229  5.08349  4.60971  3.06551  6.13143  5.07324      2 M - - -
+          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
+          0.00789  5.24168  5.96402  0.61958  0.77255  0.48576  0.95510
+      2   2.99847  5.45014  3.27203  2.07063  4.77535  3.77916  3.41979  4.24359  1.56304  2.95943  4.49700  3.04477  4.17116  3.06766  2.04612  2.97168  2.59235  3.33183  3.94979  4.49984      3 k - - -
+          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
+          0.00789  5.24168  5.96402  0.61958  0.77255  0.48576  0.95510
+      3   1.97451  2.86441  4.37757  3.79500  3.64196  4.10876  4.40327  2.69682  3.69193  2.08968  2.48275  3.47971  3.76514  3.50251  2.76431  2.59917  3.25750  2.79064  2.60378  3.94518      4 a - - -
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+          0.00789  5.24168  5.96402  0.61958  0.77255  0.48576  0.95510
+      4   2.34578  3.43634  3.51020  2.95041  4.23836  3.86833  3.32320  3.63223  2.69356  2.93198  4.12353  2.84460  2.23165  3.27576  3.37678  2.38768  2.01469  3.00363  5.57285  3.24846      5 t - - -
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+          0.74513  1.14403  1.57603  1.82621  0.17557  0.48576  0.95510
+      5   1.53771  4.86925  3.47794  2.91911  4.07551  3.04518  4.02223  2.69730  2.46110  3.12551  3.97897  3.39800  3.57801  3.23448  3.32732  2.31519  2.57901  2.75837  5.43441  4.14974     25 a - - -
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+          0.03467  5.01324  3.59608  0.61958  0.77255  1.03579  0.43842
+      6   2.91432  4.34907  4.54359  3.94893  3.42389  4.04092  3.28417  2.78503  3.79394  2.11748  2.31440  4.08505  4.40770  3.98940  3.91755  2.67188  3.14645  2.12134  1.66633  3.74848     26 w - - -
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+          0.77287  1.51044  1.14728  0.68239  0.70402  0.69201  0.69428
+      7   2.64747  4.37834  4.26814  3.69420  3.50069  3.97178  4.31414  2.36928  3.58897  1.71096  3.47684  3.93737  1.78187  3.82938  3.80431  3.26458  2.71533  2.13145  5.04495  3.85105     29 l - - -
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+          0.01292  4.75143  5.47378  0.61958  0.77255  0.46982  0.98113
+      8   2.96053  4.37627  4.68759  4.08875  3.08355  3.15739  4.42808  2.54411  3.92389  1.55658  3.49434  4.18501  4.46975  4.09969  4.01662  2.31114  2.42600  1.64838  5.00044  3.81811     30 l - - -
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+          0.03537  5.17052  3.53800  0.61958  0.77255  0.70619  0.68027
+     19   2.32206  2.15645  4.89457  4.28478  3.02969  3.41512  4.49060  2.78461  4.08437  2.05044  2.93492  4.29937  4.52109  4.22801  4.11558  3.46602  2.87194  1.42544  5.00302  3.82544     41 v - - -
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+          0.03036  5.14386  3.72670  0.61958  0.77255  0.77440  0.61801
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+          0.00762  5.27667  5.99901  0.61958  0.77255  0.48576  0.95510
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+          0.00762  5.27667  5.99901  0.61958  0.77255  0.48576  0.95510
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+          0.00762  5.27667  5.99901  0.61958  0.77255  0.48576  0.95510
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+          0.00762  5.27667  5.99901  0.61958  0.77255  0.48576  0.95510
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+          0.00762  5.27667  5.99901  0.61958  0.77255  0.48576  0.95510
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+          0.00762  5.27667  5.99901  0.61958  0.77255  0.48576  0.95510
+    131   3.18551  4.55144  5.11562  4.51003  3.23691  4.37526  4.71538  1.61876  3.08063  1.59524  3.62097  4.52327  4.72660  4.44779  4.33644  3.69006  3.41835  1.35937  5.20434  3.44126    317 v - - -
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+          0.00762  5.27667  5.99901  0.61958  0.77255  0.48576  0.95510
+    132   5.01008  6.46474  5.85869  5.92791  6.75543  0.04474  6.75680  6.83030  6.21752  6.19298  7.29548  6.03342  5.83983  6.45423  6.16114  5.23980  5.55300  6.15698  7.36342  6.94750    318 G - - -
+          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
+          0.09407  5.24168  2.47117  0.61958  0.77255  0.48576  0.95510
+    133   4.17773  6.17563  4.92320  3.86812  5.85828  4.65635  3.42635  5.06843  0.52079  4.34247  5.24879  4.14383  4.94432  3.44830  1.66123  4.13477  4.23584  4.77474  6.24460  5.22067    319 K - - -
+          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
+          0.27774  5.15621  1.44080  0.61958  0.77255  0.74360  0.64511
+    134   4.02716  5.95610  4.70758  3.75950  5.63196  4.46807  4.21944  4.88920  1.98700  4.19037  5.11519  4.02504  4.79771  3.35299  0.45026  4.00605  4.11167  4.59868  6.09064  5.07391    320 R - - -
+          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
+          0.01124  4.88971  5.61206  0.61958  0.77255  1.08458  0.41256
+    135   2.86128  3.84541  3.39667  2.83675  4.13611  2.64838  3.96371  3.52925  2.34027  3.17539  4.01738  3.32527  4.12308  3.15340  2.52366  1.84032  3.10146  1.96870  5.46237  4.16589    321 s - - -
+          2.68691  4.44704  2.77582  2.71951  3.46661  2.40245  3.72980  3.31039  2.68840  2.68576  4.25171  2.90204  2.73966  3.16600  2.88775  2.38159  2.79406  2.97763  4.55780  3.61108
+          1.13507  0.38772        *  4.52970  0.01084  0.00000        *
+//