bio-bigbio 0.1.2 → 0.1.3

data/README.md

@@ -0,0 +1,96 @@
+# BIGBIO
+
+BigBio = BIG DATA for Ruby
+
+BigBio is an initiative to a create high performance libraries for big data
+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.
+
+# Overview
+
+* BigBio can translate nucleotide sequences to amino acid
+  sequences using an EMBOSS C function, or BioRuby's translator.
+* 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.
+
+# Examples
+
+## Iterate through a FASTA file
+
+Read a file without loading the whole thing in memory
+
+```ruby
+fasta = FastaReader.new(fn)
+fasta.each do | rec |
+  print rec.descr,rec.seq
+end
+```
+
+Write a FASTA file. Any object can be passed in, as long
+as it responds to 'descr' and 'seq.to_s', or 'id' and 'seq.to_s'. E.g.
+
+```ruby
+class StorageObject
+  attr_accessor :descr, :seq
+end
+
+mysequence = StorageObject.new
+mysequence.descr = 'Test'
+mysequence.seq = "agtcta"
+```
+
+now we can write a FASTA file
+
+```ruby
+fasta = FastaWriter.new(fn)
+fasta.write(mysequence)
+```
+
+## Fetch ORFs from a sequence
+
+BigBio can parse a sequence for ORFs. Together with the FastaReader
+little memory gets used
+
+```ruby
+predictorf = PredictORF.new(id,descr,"ATCATTAGCAACACCAGCTTCCTCTCTCTCGCTTCAAAGTTCACTACTCGTGGATCTCGT")
+# get all ORFs between start and stop codons, longer than 30 bps
+orfs = predictorf.startstop(30)
+# get all sequences between stop codons
+seqs = predictorf.stopstop(0)
+```
+
+## Rapid DNA/RNA to amino acid translation
+
+Translate with EMBOSS C library, if linked, otherwise use BioRuby
+
+```ruby
+trn_table = Bio::Big::TranslationAdapter.translation_table(1)
+translate = Nucleotide::Translate.new(trn_table)
+aa_frames = translate.aa_6_frames("ATCATTAGCAACACCAGCTTCCTCTCTCTCGCTTCAAAGTTCACTACTCGTGGATCTCGT")
+```
+
+# Install
+
+The easy way
+
+```sh
+gem install bio-bigbio
+```
+
+in your code
+
+```ruby
+require 'bigbio'
+```
+
+# Copyright
+
+Copyright (c) 2011-2012 Pjotr Prins. See LICENSE for further details.
+

data/VERSION

@@ -1 +1 @@
-0.1.2
+0.1.3

data/bio-bigbio.gemspec

@@ -5,23 +5,23 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-bigbio"
-  s.version = "0.1.2"
+  s.version = "0.1.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Pjotr Prins"]
-  s.date = "2012-01-30"
+  s.date = "2012-02-03"
   s.description = "Fasta reader, ORF emitter, sequence translation"
   s.email = "pjotr.public01@thebird.nl"
   s.executables = ["getorf", "nt2aa.rb"]
   s.extra_rdoc_files = [
     "LICENSE",
-    "README.rdoc"
+    "README.md"
   ]
   s.files = [
     "Gemfile",
     "Gemfile.lock",
     "LICENSE",
-    "README.rdoc",
+    "README.md",
     "Rakefile",
     "VERSION",
     "bin/getorf",

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

@@ -7,10 +7,15 @@ class FastaWriter
     @f = File.open(fn,"w")
   end
 
-  # write a FASTA item
+  # write a FASTA item. An itex should respond to descr and seq,
+  # or id and seq
   def write item
-    @f.write ">"+item.id+' '+item.descr+"\n"
-    @f.write item.seq.strip+"\n"
+    if item.respond_to?(:descr)
+      @f.write ">"+item.descr+"\n"
+    else
+      @f.write ">"+item.id+"\n"
+    end
+    @f.write item.seq.to_s.strip+"\n"
   end
 
   def close

data/lib/bigbio/sequence/predictorf.rb

@@ -81,7 +81,7 @@ class PredictORF
 
   include Bio::Big::FrameCodonHelpers 
 
-  def initialize id, descr, seq, trn_table
+  def initialize id, descr, seq, trn_table = nil
     @id        = id
     @descr     = descr
     @seq       = seq.gsub(/\s/,'')

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-bigbio
 version: !ruby/object:Gem::Version
-  version: 0.1.2
+  version: 0.1.3
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-01-30 00:00:00.000000000Z
+date: 2012-02-03 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &27003400 !ruby/object:Gem::Requirement
+  requirement: &13483940 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: 1.4.1
   type: :runtime
   prerelease: false
-  version_requirements: *27003400
+  version_requirements: *13483940
 - !ruby/object:Gem::Dependency
   name: bio-logger
-  requirement: &27002560 !ruby/object:Gem::Requirement
+  requirement: &13483220 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: 0.9.0
   type: :runtime
   prerelease: false
-  version_requirements: *27002560
+  version_requirements: *13483220
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &27001520 !ruby/object:Gem::Requirement
+  requirement: &13482380 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *27001520
+  version_requirements: *13482380
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &26974980 !ruby/object:Gem::Requirement
+  requirement: &13467960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -54,10 +54,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *26974980
+  version_requirements: *13467960
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &26974040 !ruby/object:Gem::Requirement
+  requirement: &13466160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +65,10 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: *26974040
+  version_requirements: *13466160
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &26972580 !ruby/object:Gem::Requirement
+  requirement: &13465220 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,7 +76,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *26972580
+  version_requirements: *13465220
 description: Fasta reader, ORF emitter, sequence translation
 email: pjotr.public01@thebird.nl
 executables:
@@ -85,12 +85,12 @@ executables:
 extensions: []
 extra_rdoc_files:
 - LICENSE
-- README.rdoc
+- README.md
 files:
 - Gemfile
 - Gemfile.lock
 - LICENSE
-- README.rdoc
+- README.md
 - Rakefile
 - VERSION
 - bin/getorf
@@ -139,7 +139,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1176702177880796219
+      hash: -2925433248995829761
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:

data/README.rdoc

@@ -1,28 +0,0 @@
-= BIGBIO
-
-BigBio = BIG DATA for Ruby
-
-BigBio is an initiative to a create high performance libraries for big data
-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.
-
-== Functionality
-
-* BigBio can translate nucleotide sequences to amino acid
-  sequences using an EMBOSS C function, or BioRuby's translator.
-
-* 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.
-
-== Copyright
-
-Copyright (c) 2011-2012 Pjotr Prins. See LICENSE for further details.
-