bio-bigbio 0.1.4 → 0.1.5

data/.travis.yml

@@ -0,0 +1,12 @@
+language: ruby
+rvm:
+  - 1.9.2
+#  - 1.9.3
+#  - 1.8.7
+#  - jruby-19mode # JRuby in 1.9 mode
+#  - rbx-19mode
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/LICENSE.txt

@@ -0,0 +1,20 @@
+Copyright (c) 2011-2013 Pjotr Prins
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

@@ -8,31 +8,119 @@ computing in biology.
 BigBio may use BioLib C/C++/D functions for increasing performance and
 reducing memory consumption.
 
-This is an experimental project. If you wish to contribute subscribe
-to the BioRuby and/or BioLib mailing lists.
+In a way, this is an experimental project. I use it for
+experimentation, but what is in here should work fine. If you wish to
+contribute subscribe to the BioRuby and/or BioLib mailing lists
+instead.
 
 # Overview
 
 * BigBio can translate nucleotide sequences to amino acid
   sequences using an EMBOSS C function, or BioRuby's translator.
+* BigBio has a terrific FASTA file emitter which iterates FASTA files and
+  iterates sequences without loading everything in memory. There is
+  also an indexed edition
+* BioBio has a flexible FASTA filter 
 * BigBio has an ORF emitter which parses DNA/RNA sequences and emits
   ORFs between START_STOP or STOP_STOP codons.
-* BigBio has a FASTA file emitter, with iterates FASTA files and
-  iterates sequences without loading everything in memory.
+* BigBio has a Phylip (PAML style) emitter and writer
 
-# Examples
+# Installation
+
+The easy way
+
+```sh
+gem install bio-bigbio
+```
+
+in your code
+
+```ruby
+require 'bigbio'
+```
+
+# Command line tools
+
+Some functionality comes also as executable command line tools (see the
+./bin directory). Use the -h switch to get information. Current tools
+are 
+
+1. getorf: fetch all areas between start-stop and stop-stop codons in six frames (using EMBOSS when biolib is available)
+2. nt2aa.rb: translate in six frames (using EMBOSS when biolib is available)
+3. fasta_filter.rb
+
+## Command line Fasta Filter
+
+The CLI filter accepts standard Ruby commands. 
+
+Filter sequences that contain more than 25% C's
+
+```sh
+fasta_filter.rb --filter "rec.seq.count('C') > rec.seq.size*0.25" test/data/fasta/nt.fa
+```
+
+Look for IDs containing -126 and sequences ending on CCC
+
+```sh
+fasta_filter.rb --filter "rec.id =~ /-126/ or rec.seq =~ /CCC$/" test/data/fasta/nt.fa
+```
+
+Filter out all masked sequences that contain more than 10% masked
+nucleotides
+
+```sh
+fasta_filter.rb --filter "rec.seq.count('N')<rec.seq.size*0.10" 
+```
+
+Next to rec.id and rec.seq, you have rec.descr and 'num' as variables,
+so to skip every other record
+
+```sh
+fasta_filter.rb --filter "num % 2 == 0" 
+```
+
+Rewrite all sequences to lower case, you can use the useful rewrite
+option
+
+```sh
+fasta_filter.rb --rewrite 'rec.seq = rec.seq.downcase'
+```
+
+Filters and rewrites can be combined. The rest is up to your imagination!
+
+# API Examples
 
 ## Iterate through a FASTA file
 
 Read a file without loading the whole thing in memory
 
 ```ruby
+require 'bigbio'
+
 fasta = FastaReader.new(fn)
 fasta.each do | rec |
   print rec.descr,rec.seq
 end
 ```
 
+Since FastaReader parses the ID, write a tab file with id and sequence
+
+```ruby
+i = 1
+print "num\tid\tseq\n"
+FastaReader.new(fn).each do | rec |
+  if rec.id =~ /(AT\w+)/
+    print i,"\t",$1,"\t",rec.seq,"\n"
+    i += 1
+  end
+end
+```
+
+wich, for example, can be turned into RDF with the
+[bio-table](https://github.com/pjotrp/bioruby-table) biogem.
+
+## Write a FASTA file
+
 Write a FASTA file. The simple way
 
 ```ruby
@@ -60,6 +148,44 @@ fasta = FastaWriter.new(fn)
 fasta.write(mysequence)
 ```
 
+## Transform a FASTA file
+
+You can combine above FastaReader and FastaWriter to transform
+sequences, e.g.
+
+```ruby
+fasta = FastaWriter.new(in_fn)
+FastaReader.new(out_fn).each do | rec |
+  # Strip the description down to the second ID
+  (id1,id2) = /(\S+)\s+(\S+)/.match(rec.descr)
+  fasta.write(id2,rec.seq)
+end
+```
+
+The downside to this approach is the explicit file naming. What if you
+want to use STDIN or some other source instead? I have come round to
+the idea of using a combination of lambda and block. For example:
+
+```ruby
+  FastaReader::emit_fastarecord(-> {gets}) { |rec|
+    print FastaWriter.to_fasta(rec)
+  }
+```
+
+which takes STDIN line by line, and outputs FASTA on STDOUT. This is 
+a better design as the FastaReader and FastaWriter know nothing of
+the mechanism fetching and displaying data. These can both be 'pure' 
+functions. Note also that the data is never fully loaded into RAM.
+
+Here the transformer functional style
+
+```ruby
+  FastaReader::emit_fastarecord(-> {gets}) { |rec|
+    (id1,id2) = /(\S+)\s+(\S+)/.match(rec.descr)
+    print FastaWriter.to_fasta(id2,req.seq)
+  }
+```
+
 ## Fetch ORFs from a sequence
 
 BigBio can parse a sequence for ORFs. Together with the FastaReader
@@ -83,21 +209,27 @@ translate = Nucleotide::Translate.new(trn_table)
 aa_frames = translate.aa_6_frames("ATCATTAGCAACACCAGCTTCCTCTCTCTCGCTTCAAAGTTCACTACTCGTGGATCTCGT")
 ```
 
-# Install
+# Project home page
 
-The easy way
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
 
-```sh
-gem install bio-bigbio
-```
+  http://github.com/pjotrp/bigbio
 
-in your code
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
 
-```ruby
-require 'bigbio'
-```
+# Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+# Biogems.info
+
+This Biogem is published at [#bio-table](http://biogems.info/index.html)
 
 # Copyright
 
-Copyright (c) 2011-2012 Pjotr Prins. See LICENSE for further details.
+Copyright (c) 2011-2013 Pjotr Prins. See LICENSE for further details.
 

data/Rakefile

@@ -37,6 +37,7 @@ RSpec::Core::RakeTask.new(:rcov) do |spec|
   spec.rcov = true
 end
 
+task :test => :spec
 task :default => :spec
 
 require 'rake/rdoctask'

data/VERSION

@@ -1 +1 @@
-0.1.4
+0.1.5

data/bin/fasta_filter.rb

@@ -0,0 +1,100 @@
+#! /usr/bin/env ruby
+#
+# Filter for FASTA files
+#
+
+$: << File.dirname(__FILE__)+'/../lib'
+
+require 'bigbio'
+require 'optparse'
+require 'ostruct'
+
+class OptParser
+  #
+  # Return a structure describing the options.
+  #
+  def self.parse(args)
+    # The options specified on the command line will be collected in *options*.
+    # We set default values here.
+    options = OpenStruct.new
+    options.codonize = false
+    options.verbose = false
+
+    opt_parser = OptionParser.new do |opts|
+      opts.banner = "Usage: fasta_filter.rb [options]"
+
+      opts.separator ""
+      opts.separator "Specific options:"
+
+      opts.on("--filter expression","Filter on Ruby expression") do |expr|
+        options.filter = expr
+      end
+
+      opts.on("--rewrite expression","Rewrite expression") do |expr|
+        options.rewrite = expr
+      end
+
+      opts.on("--codonize",
+              "Trim sequence to be at multiple of 3 nucleotides") do |b|
+        options.codonize = b
+      end
+
+      opts.on("--min size",
+              "Set minimum sequence size") do |min|
+        options.min = min.to_i
+      end
+
+      opts.on("--id","Write out ID only") do |b|
+        options.id = b
+      end
+
+      opts.on("-v", "--[no-]verbose", "Run verbosely") do |v|
+        options.verbose = v
+      end
+
+      opts.separator ""
+      opts.separator "Examples:"
+      opts.separator ""
+      opts.separator "  fasta_filter.rb --filter \"rec.id =~ /-126/ or rec.seq =~ /CCC$/\" test/data/fasta/nt.fa"
+      opts.separator "  fasta_filter.rb --filter \"rec.seq.count('C') > rec.seq.size*0.25\" test/data/fasta/nt.fa"
+      opts.separator "  fasta_filter.rb --filter \"rec.descr =~ /C. elegans/\" test/data/fasta/nt.fa"
+      opts.separator "  fasta_filter.rb --filter \"num % 2 == 0\" test/data/fasta/nt.fa"
+      opts.separator "  fasta_filter.rb test/data/fasta/nt.fa --rewrite 'rec.seq.downcase!'"
+      opts.separator ""
+      opts.separator "Other options:"
+      opts.separator ""
+
+      opts.on_tail("-h", "--help", "Show this message") do
+        puts opts
+        exit
+      end
+
+    end
+
+    opt_parser.parse!(args)
+    options
+  end  # parse()
+end  # class OptParser
+
+options = OptParser.parse(ARGV)
+
+num = -1
+FastaReader::emit_fastarecord(-> { ARGF.gets }) { | rec |
+  num += 1
+  # --- Filtering
+  next if options.filter and not eval(options.filter)
+  if options.codonize 
+    # --- Round sequence to nearest 3 nucleotides
+    size = rec.seq.size
+    rec.seq = rec.seq[0..size - (size % 3) - 1]
+  end
+  # --- Only use sequences from MIN size
+  next if options.min and rec.seq.size < options.min
+  # --- Truncate description to ID
+  rec.descr = rec.id if options.id
+ 
+  # --- rewrite
+  eval(options.rewrite) if options.rewrite
+  print rec.to_fasta
+}
+

data/bin/fasta_sort.rb

@@ -0,0 +1,24 @@
+#!/usr/bin/env ruby
+#
+# fasta_sort: Sorts a FASTA file and outputs sorted unique records as FASTA again
+#
+# Usage:
+#
+#   fasta_sort inputfile(s)
+
+require 'bio'
+
+include Bio
+
+table = Hash.new  
+ARGV.each do | fn |
+  Bio::FlatFile.auto(fn).each do | seq |
+    table[seq.definition] ||= seq.data
+  end
+end
+
+table.sort.each do | definition, data |
+  rec = Bio::FastaFormat.new('> '+definition.strip+"\n"+data)
+  print rec
+end
+

data/bin/getorf

@@ -6,12 +6,8 @@
 # (aa_heuristic.fa and nt_heuristic.fa respectively)
 #
 # You can choose the heuristic on the command line (default stopstop).
-#
-# Author:: Pjotr Prins
-# Copyright:: 2009-2011
-# License:: Ruby License
-#
-# Copyright (C) 2009-2011 Pjotr Prins <pjotr.prins@thebird.nl>
+
+$stderr.print "WARNING: This tool has one or more known bugs! Better use the EMBOSS getorf instead for now\n"
 
 rootpath = File.dirname(File.dirname(__FILE__))
 $: << File.join(rootpath,'lib')
@@ -48,10 +44,10 @@ EXAMPLE
     exit()
   }
    
-  opts.on("-h heuristic", String, "Heuristic (stopstop)") do | s |
+  opts.on("-h heuristic", String, "Heuristic (default #{heuristic})") do | s |
     heuristic = s
   end
-  opts.on("-s size", "--min-size", Integer, "Minimal sequence size") do | n |
+  opts.on("-s size", "--min-size", Integer, "Minimal sequence size (default #{minsize})") do | n |
     minsize = n
   end
   opts.on("--longest", "Only get longest ORF match") do 

data/bin/nt2aa.rb

@@ -3,11 +3,6 @@
 # Translate nucleotide sequences into aminoacids sequences in all 
 # reading frames.
 #
-#
-# (: pjotrp 2009, 2012 rblicense :)
-#
-# Copyright (C) 2012 Pjotr Prins <pjotr.prins@thebird.nl> 
-
 USAGE =<<EOM
   ruby #{__FILE__} [--six-frame] inputfile(s)
 EOM
@@ -44,7 +39,9 @@ ARGV.each do | fn |
 
         # ajpseqt  = Biolib::Emboss.ajTrnSeqOrig(trnTable,ajpseq,frame)
         # aa       = Biolib::Emboss.ajSeqGetSeqCopyC(ajpseqt)
-        print "> ",rec.descr," [",frame.to_s,"]\n"
+        print ">",rec.descr
+        print " [",frame.to_s,"]" if do_sixframes
+        print "\n"
         print aa,"\n"
     end
   }

data/bio-bigbio.gemspec

@@ -5,25 +5,28 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-bigbio"
-  s.version = "0.1.4"
+  s.version = "0.1.5"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Pjotr Prins"]
-  s.date = "2012-02-03"
+  s.date = "2013-05-03"
   s.description = "Fasta reader, ORF emitter, sequence translation"
   s.email = "pjotr.public01@thebird.nl"
-  s.executables = ["getorf", "nt2aa.rb"]
+  s.executables = ["fasta_filter.rb", "fasta_sort.rb", "getorf", "nt2aa.rb"]
   s.extra_rdoc_files = [
-    "LICENSE",
+    "LICENSE.txt",
     "README.md"
   ]
   s.files = [
+    ".travis.yml",
     "Gemfile",
     "Gemfile.lock",
-    "LICENSE",
+    "LICENSE.txt",
     "README.md",
     "Rakefile",
     "VERSION",
+    "bin/fasta_filter.rb",
+    "bin/fasta_sort.rb",
     "bin/getorf",
     "bin/nt2aa.rb",
     "bio-bigbio.gemspec",
@@ -42,6 +45,7 @@ Gem::Specification.new do |s|
     "lib/bigbio/db/fasta/fastarecord.rb",
     "lib/bigbio/db/fasta/fastawriter.rb",
     "lib/bigbio/db/fasta/indexer.rb",
+    "lib/bigbio/db/phylip.rb",
     "lib/bigbio/environment.rb",
     "lib/bigbio/sequence/predictorf.rb",
     "lib/bigbio/sequence/translate.rb",

data/lib/bigbio/db/fasta/fastareader.rb

@@ -130,3 +130,38 @@ class FastaReader
   end
 
 end
+
+# The following is actually a module/trait implementation without state
+
+class FastaReader
+
+  # func passes in a FASTA buffer. Every time a record is parsed it is 
+  # yielded.
+  #
+  def FastaReader::emit getbuf_func
+    seq = ""
+    id = nil
+    descr = nil
+    while buf = getbuf_func.call
+      buf.split(/\n/).each do | line |
+        if line =~ /^>/
+          yield id, descr, seq if descr
+          descr = line[1..-1].strip
+          matched = /^(\S+)/.match(descr)
+          id = matched[0]
+          seq = ""
+        else
+          seq += line.strip
+        end
+      end
+    end
+    yield id, descr, seq if descr and seq.size > 0
+  end
+
+  def FastaReader::emit_fastarecord getbuf_func
+    emit(getbuf_func) do | id, descr, seq |
+      yield FastaRecord.new(id, descr, seq) 
+    end
+  end
+
+end

data/lib/bigbio/db/fasta/fastarecord.rb

@@ -7,6 +7,10 @@ class FastaRecord
     @descr = descr
     @seq = seq
   end
+
+  def to_fasta
+    ">"+@descr+"\n"+@seq+"\n"
+  end
 end
 
 class FastaPairedRecord
@@ -30,7 +34,9 @@ class FastaPairedRecord
     if nt.seq.size == aa.seq.size*3-3
       aa.seq.chop!
     end
-    raise "Sequence size mismatch for #{nt.id} <nt:#{nt.seq.size} != #{aa.seq.size*3} (aa:#{aa.seq.size}*3)>" if nt.seq.size != aa.seq.size*3
+    nt_size = nt.seq.size
+    expected_size = aa.seq.size*3
+    # raise "Sequence size mismatch for #{nt.id} <nt:#{nt.seq.size} != #{aa.seq.size*3} (aa:#{aa.seq.size}*3)>" if expected_size - 3 > nt_size and  nt_size > expected_size + 3
   end
 
   def id

data/lib/bigbio/db/phylip.rb

@@ -0,0 +1,49 @@
+# Simple phylip reader. Supports PAML style files formatted as
+#
+# sequence 1
+# AAGCTTCACCGGCGCAGTCATTCTCATAAT
+# CGCCCACGGACTTACATCCTCATTACTATT
+# sequence 2
+# AAGCTTCACCGGCGCAATTATCCTCATAAT
+# CGCCCACGGACTTACATCCTCATTATTATT
+# sequence 3
+# AAGCTTCACCGGCGCAGTTGTTCTTATAAT
+# TGCCCACGGACTTACATCATCATTATTATT
+# sequence 4
+# AAGCTTCACCGGCGCAACCACCCTCATGAT
+# TGCCCATGGACTCACATCCTCCCTACTGTT
+
+module Bio
+  module Big
+    module PhylipReader
+      # Define get_line as a lambda function, e.g.
+      #   Bio::Big::PhylipReader.emit_seq(-> { lines.next }) { | name, seq | p [name,seq] }
+
+      def PhylipReader::emit_seq get_line
+        line = get_line.call.strip
+        a = line.split
+        seq_num = a[0].to_i
+        seq_size = a[1].to_i
+        name = nil
+        seq = ""
+        while true
+          line = get_line.call
+          break if line == nil or line == ""
+          line = line.strip
+          if name == nil
+            name = line
+            next
+          end
+          seq += line
+          if seq.size >= seq_size
+            raise "Name wrong size for #{name}" if name.size > 20
+            raise "Sequence wrong size for #{name}" if seq.size > seq_size
+            yield name, seq
+            name = nil
+            seq = ""
+          end
+        end
+      end
+    end
+  end
+end

data/spec/emitter_spec.rb

@@ -20,6 +20,23 @@ describe Bio::Big::FastaEmitter, "when using the emitter" do
     end
   end
 
+  it "should emit functional style" do
+    count = 0
+    FastaReader::emit_fastarecord(-> { File.open("test/data/fasta/nt.fa").read }) { |rec|
+      case count
+        when 0
+          rec.id.should == "PUT-157a-Arabidopsis_thaliana-1"
+          rec.seq[0..10].should == "AGGTTCGNACG"
+        when 1
+          rec.id.should == "PUT-157a-Arabidopsis_thaliana-2"
+          rec.seq[0..10].should == "AGACAAACGAC"
+        else
+          break
+      end
+      count += 1
+    }
+  end
+
   it "should emit large parts" do 
     FastaEmitter.new("test/data/fasta/nt.fa").emit_seq do | part, index, tag, seq |
       # p [index, part, tag, seq]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-bigbio
 version: !ruby/object:Gem::Version
-  version: 0.1.4
+  version: 0.1.5
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-02-03 00:00:00.000000000Z
+date: 2013-05-03 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &15446660 !ruby/object:Gem::Requirement
+  requirement: &27203900 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: 1.4.1
   type: :runtime
   prerelease: false
-  version_requirements: *15446660
+  version_requirements: *27203900
 - !ruby/object:Gem::Dependency
   name: bio-logger
-  requirement: &15445800 !ruby/object:Gem::Requirement
+  requirement: &27203120 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: 0.9.0
   type: :runtime
   prerelease: false
-  version_requirements: *15445800
+  version_requirements: *27203120
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &15445180 !ruby/object:Gem::Requirement
+  requirement: &27202300 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *15445180
+  version_requirements: *27202300
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &15444540 !ruby/object:Gem::Requirement
+  requirement: &27201380 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -54,10 +54,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *15444540
+  version_requirements: *27201380
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &15443800 !ruby/object:Gem::Requirement
+  requirement: &27200760 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +65,10 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: *15443800
+  version_requirements: *27200760
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &15440240 !ruby/object:Gem::Requirement
+  requirement: &27199840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,23 +76,28 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *15440240
+  version_requirements: *27199840
 description: Fasta reader, ORF emitter, sequence translation
 email: pjotr.public01@thebird.nl
 executables:
+- fasta_filter.rb
+- fasta_sort.rb
 - getorf
 - nt2aa.rb
 extensions: []
 extra_rdoc_files:
-- LICENSE
+- LICENSE.txt
 - README.md
 files:
+- .travis.yml
 - Gemfile
 - Gemfile.lock
-- LICENSE
+- LICENSE.txt
 - README.md
 - Rakefile
 - VERSION
+- bin/fasta_filter.rb
+- bin/fasta_sort.rb
 - bin/getorf
 - bin/nt2aa.rb
 - bio-bigbio.gemspec
@@ -111,6 +116,7 @@ files:
 - lib/bigbio/db/fasta/fastarecord.rb
 - lib/bigbio/db/fasta/fastawriter.rb
 - lib/bigbio/db/fasta/indexer.rb
+- lib/bigbio/db/phylip.rb
 - lib/bigbio/environment.rb
 - lib/bigbio/sequence/predictorf.rb
 - lib/bigbio/sequence/translate.rb
@@ -139,7 +145,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -2436097965031091716
+      hash: 2941883289909211187
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:

data/LICENSE

@@ -1,34 +0,0 @@
-If a license is not specified the code contributed to BioBig defaults to the
-BSD license:
-
-Copyright (c) 2008, 2009 The BioLib Project
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-    * Redistributions of source code must retain the above copyright notice,
-      this list of conditions and the following disclaimer.
-
-    * Redistributions in binary form must reproduce the above copyright notice,
-      this list of conditions and the following disclaimer in the documentation
-      and/or other materials provided with the distribution.
-
-    * Neither the name of the The BioLib Project nor the names of
-      its contributors may be used to endorse or promote products derived from
-      this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
-ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-For more information on opensource software licenses see
-http://www.opensource.org/licenses/bsd-license.php,
-http://www.gnu.org/licenses/gpl.html and http://www.fsf.org/.