bio-bigbio 0.1.1

data/test/doctest/test_fasta.rb

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+# Ruby DocTest
+#
+# BioBig FastaReader and FastaWriter implementation
+#
+# Run with ./runner.rb or
+# 
+#   ../../../biolib/tools/rubydoctest/bin/rubydoctest test_fasta.rb
+#
+# Documentation with rd2 -r rd/rd2html-lib *.rb
+
+cwd = File.dirname(__FILE__)
+Dir.chdir(cwd)
+
+# $: << '../../../mappings/swig/ruby/biolib_core/'
+# $: << '../../../mappings/swig/ruby/biolib_R/'
+
+# require 'biolib/biolib_core'
+
+# Biolib::Biolib_core.biolib_setloglevel(7)
+
+if $UNITTEST
+
+=begin
+
+  >> $: << '../../lib'
+  >> require 'bigbio'
+  >> TESTDIR = '../data/fasta'
+  >> nt_FILE = TESTDIR + "/nt.fa"
+  >> AA_FILE = TESTDIR + "/aa.fa"
+
+BioLib's reference FASTA reader and writer contain a number of useful properties.
+First RAM usage is limited. Second the interface is simple and to the point.
+
+Open a reader and walk the file to find a FASTA record
+
+  !> include ::BioBig
+  >> nt_in = FastaReader.new(nt_FILE)
+  >> fastarec = nil
+  >> nt_in.each { | rec | fastarec = rec if rec.id =~ /-Arabidopsis_thaliana-126/ }
+  >> fastarec.id
+  => "PUT-157a-Arabidopsis_thaliana-126"
+
+Open a writer and write the record
+
+  >> nt_out = FastaWriter.new("nt.fa")
+  >> nt_out.write fastarec
+  >> nt_out.close
+
+Cleanup 
+
+  >> File.unlink("nt.fa")
+
+The ID in the FASTA file can vary between implementations. Therefore a regex is
+allowed to find the ID - the default is /^(\S+)/ - or the first non-white space
+making up the tag. Here we grab the first relevant number
+
+  >> nt_in = FastaReader.new(nt_FILE, :regex => '(\d+)\s')
+  >> nt_in.each { | rec | fastarec = rec if rec.id == "126" }
+  >> fastarec.id
+  => "126"
+
+In the first examples the FastaReader parses the whole file on demand. When
+we use the :index option an indexer is built up at the same time (or the 
+first time an indexing function is used). So
+
+  >> nt_in = FastaReader.new(nt_FILE, :regex => '(\d+)\s', :index => true)
+  >> rec = nt_in.get("122")
+  >> rec.id
+  => "122"
+
+Fetching more information from the FASTA file does not parse the whole file
+again
+
+  >> nt_in.get("121").id
+  => "121"
+  >> nt_in.get("121").seq
+  => "CAATTTTTTAAACATTTACTGGTTACTAAATTTGGAGATAGTATCACATTTCTAAAGGGTAAGTTGGAAAATAAATTTACAGAAAAATTATAAGTATAAAAAGTATACAGATGGATTACTTAGACAGCAGCGGGTGTGGGGGCTGATGCGGAGTGGTCGTGGTCGAAGAAGGAACCCGGTTTCCGGGGGGATCTCAGTAAACTCGGAAAGAATGGCCCGAATTCGTCACCGCCAACTAGTTCTTCCTCGAGAAGCACTTCAACGAGCTTATCATGGGCTTCACGATTGTTCTTTATGTGGGTTAGAGCTATCTCATATGCACTGGCTGATAGTTTCTTCACCGGCAGAATCAATGTCTTCTGGAAGCTTCTCAGAAATGGAGTTTCTTGGCACCATCCT"
+
+It is also possible to fetch a numbered record
+
+  >> rec = nt_in.get_by_index(0)
+  >> rec.id
+  => "1"
+  >> rec.descr
+  => "PUT-157a-Arabidopsis_thaliana-1\tPlantGDB-assembled Unique Transcript-fragment derived from Arabidopsis_thaliana mRNAs Jan_15_2007 (based on GenBank release 157)."
+
+=end
+
+
+$: << '../../lib'
+require 'biobig'
+require 'test/unit'
+
+TESTDIR = '../../../test/data/fasta'
+nt_FILE = TESTDIR + "/nt.fa"
+AA_FILE = TESTDIR + "/aa.fa"
+
+class TestBiolibFasta < Test::Unit::TestCase
+
+  def setup
+  end
+
+  def test_indexer
+    nt_in = FastaReader.new(nt_FILE, :regex => '(\d+)\s', :index => true)
+    rec = nt_in.get("122")
+    assert_equal("122",rec.id)
+    assert_equal("121",nt_in.get("121").id)
+  end
+
+end
+
+end # $UNITTEST

data/test/doctest/test_frames.rb

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+# Ruby DocTest
+#
+# Translate a nucleotide sequence into six reading frames using the fast
+# EMBOSS transeq function
+#
+# Run with ./runner.rb or
+#
+#   env DATA=../../../biolib/src/test/data/emboss/ ruby ../../../biolib/tools/rubydoctest/bin/rubydoctest test_getorf.rb
+#
+# or
+#
+#   ruby ../../../biolib/tools/rubydoctest/bin/rubydoctest test_getorf.rb
+#
+# Documentation with rd2 -r rd/rd2html-lib *.rb
+
+cwd = File.dirname(__FILE__)
+Dir.chdir(cwd)
+
+$: << "../../lib"
+
+if $UNITTEST
+
+=begin
+
+BibBio's frame translation uses the rapid Biolib::Emboss::transeq function to
+translate Nucleotide sequences to Amino Acid sequences. 
+
+  >> require 'bigbio/sequence/translate'
+
+  >> id = "PUT-157a-Arabidopsis_thaliana-126"
+  >> descr = "PlantGDB Arabidopsis_thaliana Jan_15_2007"
+  >> sequence = "ATCATTAGCAACACCAGCTTCCTCTCTCTCGCTTCAAAGTTCACTACTCGTGGATCTCGT
+                 CTTCAGTGTACAGTATCAAGGGCTCGATCTGCGGTGGATGAGACATCAGATTCAGGAGCT
+                 TTTCAAAGAACTGCATCGACATCCGTAACTTCGTTTCAAAAGATTCCAATTCTCAGTTTC
+                 AGCTGAATCTGGTAGATACCATCTTTACATATCGTATGCTTGTCATGGGCTTCTAGATGC
+                 CTTTCATACTTAAAGATCAAAGGACTTGACGATGCAATAAGCTTCTCGTCTGTAAAACCC"
+
+
+   >> translate = Nucleotide::Translate.new(1)
+   >> list = translate.aa_frames(sequence)
+
+We should have six frames
+
+   >> list.size
+   => 6
+
+   >> aa = list.first
+   >> aa[:frame]
+   => 1
+
+This result matches the one from the EMBOSS web interface:
+
+   >> aa[:sequence] 
+   => "IISNTSFLSLASKFTTRGSRLQCTVSRARSAVDETSDSGAFQRTASTSVTSFQKIPILSFS*IW*IPSLHIVCLSWASRCLSYLKIKGLDDAISFSSVKP"
+
+=end
+
+
+$: << '..'
+require 'db/fasta'
+require 'test/unit'
+
+TESTDIR = '../../../test/data/fasta'
+AA_FILE = TESTDIR + "/aa.fa"
+
+# class TestBiolibFasta < Test::Unit::TestCase
+# 
+#   def setup
+#   end
+# 
+#   def test_indexer
+#   end
+# 
+# end
+
+end # $UNITTEST

data/test/doctest/test_getorf.rb

@@ -0,0 +1,154 @@
+# Ruby DocTest
+#
+# Test getorf functionality.
+#
+# Run with ./runner.rb or
+#
+#   env DATA=../data/EMBOSS/ ruby ../../../biolib/tools/rubydoctest/bin/rubydoctest test_getorf.rb
+#
+# Documentation with rd2 -r rd/rd2html-lib *.rb
+
+cwd = File.dirname(__FILE__)
+Dir.chdir(cwd)
+
+$: << "../../lib"
+
+if $UNITTEST
+
+=begin
+
+BigBio's ORF predictor uses the rapid Biolib::Emboss::transeq function to
+translate Nucleotide sequences to Amino Acid sequences. Next it allows
+several heuristics to select potential ORF's and returns them with their
+reading frame and position in the nucleotide sequence. For example all
+ORF's can be returned in the six reading frames, or simply the longest one.
+
+One of the advantages of PredictORF is that it can return both the amino acid
+and exactly matching nucleotide sequences which can be useful when calculating
+dN/dS (or Ka/Ks) ratios, for example.
+
+  >> require 'bigbio/sequence/predictorf'
+
+  >> id = "PUT-157a-Arabidopsis_thaliana-126"
+  >> descr = "PlantGDB Arabidopsis_thaliana Jan_15_2007"
+  >> sequence = "ATCATTAGCAACACCAGCTTCCTCTCTCTCGCTTCAAAGTTCACTACTCGTGGATCTCGT
+                 CTTCAGTGTACAGTATCAAGGGCTCGATCTGCGGTGGATGAGACATCAGATTCAGGAGCT
+                 TTTCAAAGAACTGCATCGACATCCGTAACTTCGTTTCAAAAGATTCCAATTCTCAGTTTC
+                 AGCTGAATCTGGTAGATACCATCTTTACATATCGTATGCTTGTCATGGGCTTCTAGATGC
+                 CTTTCATACTTAAAGATCAAAGGACTTGACGATGCAATAAGCTTCTCGTCTGTAAAACCC"
+
+Pick up the EMBOSS translation table:
+
+  >> trn_table = Biolib::Emboss.ajTrnNewI(1)
+
+Initiate the ORF prediction class
+
+  >> predict = PredictORF.new(id,descr,sequence,trn_table)
+ 
+The methods return a list of ORFCandidate ordered by sequence length. Here
+we look for all ORF's between STOP codons (with a minimal size of 30 AA).
+
+  >> orflist = predict.stopstop
+  >> orflist.size
+  => 9
+
+Get the first (and largest) ORF
+
+  >> orf = orflist.first
+
+The id contains the number of the ORF at the last position (like EMBOSS' 
+getorf does)
+
+  >> orf.id
+  => "PUT-157a-Arabidopsis_thaliana-126_1"
+
+The description contains 'XX' for the STOPSTOP search. Unlike getorf it shows
+the reading frame.
+
+  >> orf.descr
+  => "[XX +1 0 - 183; 183/300] PlantGDB Arabidopsis_thaliana Jan_15_2007"
+  >> orf.aa.seq.size
+  => 61
+  >> orf.aa.seq
+  => "IISNTSFLSLASKFTTRGSRLQCTVSRARSAVDETSDSGAFQRTASTSVTSFQKIPILSFS"
+
+The ORF object contains more information:
+
+  >> orf.nt.start
+  => 0
+  >> orf.frame
+  => 1
+
+The matching sequence with the AA
+
+  >> orf.nt.seq
+  => "ATCATTAGCAACACCAGCTTCCTCTCTCTCGCTTCAAAGTTCACTACTCGTGGATCTCGTCTTCAGTGTACAGTATCAAGGGCTCGATCTGCGGTGGATGAGACATCAGATTCAGGAGCTTTTCAAAGAACTGCATCGACATCCGTAACTTCGTTTCAAAAGATTCCAATTCTCAGTTTCAGC"
+
+And it keeps track of the full nucleotide sequence
+
+  >> orf.nt.fullseq
+  => "ATCATTAGCAACACCAGCTTCCTCTCTCTCGCTTCAAAGTTCACTACTCGTGGATCTCGTCTTCAGTGTACAGTATCAAGGGCTCGATCTGCGGTGGATGAGACATCAGATTCAGGAGCTTTTCAAAGAACTGCATCGACATCCGTAACTTCGTTTCAAAAGATTCCAATTCTCAGTTTCAGCTGAATCTGGTAGATACCATCTTTACATATCGTATGCTTGTCATGGGCTTCTAGATGCCTTTCATACTTAAAGATCAAAGGACTTGACGATGCAATAAGCTTCTCGTCTGTAAAACCC"
+
+Let's check one of the others
+
+  >> orf = orflist[3]
+  >> orf.frame
+  => 3
+  >> orf.nt.start
+  => 101
+  >> orf.nt.stop
+  => 233
+  >> orf.aa.seq
+  => "DIRFRSFSKNCIDIRNFVSKDSNSQFQLNLVDTIFTYRMLVMGF"
+  >> orf.nt.seq
+  => "GACATCAGATTCAGGAGCTTTTCAAAGAACTGCATCGACATCCGTAACTTCGTTTCAAAAGATTCCAATTCTCAGTTTCAGCTGAATCTGGTAGATACCATCTTTACATATCGTATGCTTGTCATGGGCTTC"
+  >> orf.nt.fullseq[orf.nt.start..orf.nt.stop]
+  => "GACATCAGATTCAGGAGCTTTTCAAAGAACTGCATCGACATCCGTAACTTCGTTTCAAAAGATTCCAATTCTCAGTTTCAGCTGAATCTGGTAGATACCATCTTTACATATCGTATGCTTGTCATGGGCTTCT"
+
+Naming for each ORF
+
+  >> orf.id
+  => "PUT-157a-Arabidopsis_thaliana-126_6"
+  >> orf.descr
+  => "[XX +3 101 - 233; 132/300] PlantGDB Arabidopsis_thaliana Jan_15_2007"
+
+The ORF are sorted by size, so if you want to know the size of the smallest ORF
+
+  >> orflist.last.aa.seq.size
+  => 30
+
+STOPSTOP (the stopstop method above) is just one heuristic. You can use
+startstop to get a list of ORF's with START codon:
+
+  >> orflist = predict.startstop
+  >> orflist.size
+  => 0
+
+Another one is to get the longest likely ORF with
+
+  >> longest = predict.longest_startstop
+  >> longest.aa.seq.size
+  => 21
+
+
+=end
+
+
+$: << '..'
+require 'db/fasta'
+require 'test/unit'
+
+TESTDIR = '../../../test/data/fasta'
+AA_FILE = TESTDIR + "/aa.fa"
+
+# class TestBiolibFasta < Test::Unit::TestCase
+# 
+#   def setup
+#   end
+# 
+#   def test_indexer
+#   end
+# 
+# end
+
+end # $UNITTEST

data/test/doctest/test_paired.rb

@@ -0,0 +1,55 @@
+# Ruby DocTest
+#
+# Test paired nt+AA sequence functiontlity.
+#
+# Run with ./runner.rb or
+#
+#   ../../../../tools/rubydoctest/bin/rubydoctest test_paired.rb
+#
+# Documentation with rd2 -r rd/rd2html-lib *.rb
+
+cwd = File.dirname(__FILE__)
+Dir.chdir(cwd)
+
+# $: << '../../../mappings/swig/ruby/rqtl/'
+
+# require 'biolib/biolib_core'
+# Biolib::Biolib_core.biolib_setloglevel(7)
+
+if $UNITTEST
+
+=begin
+
+  >> $: << '..'
+  !> require 'bio/sequence2'
+
+Sequence pairs are paired NT and AA sequences where one can be tested against
+the other (through translation) and an nt sequence can be aligned against an AA
+alignment (protein alignment to nucleotide alignment, also known as pal2ntl).
+
+=end
+
+
+$: << '..'
+require 'db/fasta'
+require 'test/unit'
+
+TESTDIR = '../../../test/data/fasta'
+nt_FILE = TESTDIR + "/nt.fa"
+AA_FILE = TESTDIR + "/aa.fa"
+
+class TestBiolibFasta < Test::Unit::TestCase
+
+  def setup
+  end
+
+  def test_indexer
+    nt_in = FastaReader.new(nt_FILE, :regex => '(\d+)\s', :index => true)
+    rec = nt_in.get("122")
+    assert_equal("122",rec.id)
+    assert_equal("121",nt_in.get("121").id)
+  end
+
+end
+
+end # $UNITTEST

data/test/performance/translate_with_biolib.rb

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+#! /usr/bin/ruby
+#
+# Performance testing routing for translating a FASTA file into six
+# reading frames using the Biolib (EMBOSS) routines.
+#
+# by Pjotr Prins (c) 2009
+# 
+# To reduce the impact of file IO you can run multiple iterations using
+# a command line switch. 
+#
+# Usage: 
+#
+#   ruby -Ipath_to_biolib translate_with_biolib.rb --iter 10 nucleotides.fasta
+#
+# Example:
+#
+#   time ruby -I~/izip/git/opensource/biolib/lib/ translate_with_bioruby.rb --iter 10 ../data/fasta/nt.fa > test.out
+#
+# Renders on my machine:
+#
+#  96 records 5760 times translated!
+#   real    0m0.290s
+#   user    0m0.252s
+#   sys     0m0.024s
+#
+# with a large file
+#
+#  22929 records 137574 times translated!
+#   real    0m20.306s
+#   user    0m15.997s
+#   sys     0m1.344s
+
+
+$: << '../../lib'
+
+require 'biolib/emboss'
+require 'bigbio'
+
+iter=1
+fn = ARGV.shift
+
+if fn == '--iter'
+  iter = ARGV.shift.to_i
+  fn = ARGV.shift
+end
+
+nt = FastaReader.new(fn)
+trnTable = Biolib::Emboss.ajTrnNewI(1);
+
+nt.each { | rec |
+  (0..iter).each do | repeat |
+    ajpseq   = Biolib::Emboss.ajSeqNewNameC(rec.seq,"Test sequence")
+
+    [-3,-2,-1,1,2,3].each do | frame |
+      ajpseqt  = Biolib::Emboss.ajTrnSeqOrig(trnTable,ajpseq,frame)
+      aa       = Biolib::Emboss.ajSeqGetSeqCopyC(ajpseqt)
+      print "> ",rec.id," ",frame.to_s,"\n"
+      print aa,"\n"
+    end
+  end
+}
+
+$stderr.print nt.size," records ",nt.size*6*iter," times translated!"
+
+
+
+

data/test/performance/translate_with_bioruby.rb

@@ -0,0 +1,64 @@
+#! /usr/bin/ruby
+#
+# Performance testing routing for translating a FASTA file into six
+# reading frames using the Bioruby routines.
+#
+# by Pjotr Prins (c) 2009
+# 
+# To reduce the impact of file IO you can run multiple iterations using
+# a command line switch. 
+#
+# Usage: 
+#
+#   ruby -Ipath_to_bioruby translate_with_bioruby.rb --iter 10 nucleotides.fasta
+#
+# Example:
+#
+#   time ruby -I~/izip/git/opensource/bioruby/lib/ translate_with_bioruby.rb --iter 10 ../data/fasta/nt.fa > test.out
+#
+# Renders on my machine:
+#
+#  96 records 5760 times translated!
+#   real    0m6.414s
+#   user    0m5.928s
+#   sys     0m0.384s
+#
+# with a large file
+#
+#  22929 records 137574 times translated!
+#   real    9m30.952s
+#   user    8m42.877s
+#   sys     0m32.878s
+
+
+
+$: << '../../lib'
+
+require 'bio'
+require 'bigbio'
+
+iter=1
+fn = ARGV.shift
+
+if fn == '--iter'
+  iter = ARGV.shift.to_i
+  fn = ARGV.shift
+end
+
+nt = FastaReader.new(fn)
+
+nt.each { | rec |
+  (0..iter).each do | repeat |
+    seq = Bio::Sequence::NA.new(rec.seq)
+    [-3,-2,-1,1,2,3].each do | frame |
+      print "> ",rec.id," ",frame.to_s,"\n"
+      print seq.translate(frame),"\n"
+    end
+  end
+}
+
+$stderr.print nt.size," records ",nt.size*6*iter," times translated!"
+
+
+
+

metadata

@@ -0,0 +1,163 @@
+--- !ruby/object:Gem::Specification
+name: bio-bigbio
+version: !ruby/object:Gem::Version
+  version: 0.1.1
+  prerelease: 
+platform: ruby
+authors:
+- Pjotr Prins
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-01-30 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &12808920 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.1
+  type: :runtime
+  prerelease: false
+  version_requirements: *12808920
+- !ruby/object:Gem::Dependency
+  name: bio-logger
+  requirement: &12807920 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.9.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *12807920
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: &12806940 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.3.0
+  type: :development
+  prerelease: false
+  version_requirements: *12806940
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &12780320 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *12780320
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &12779320 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.5.2
+  type: :development
+  prerelease: false
+  version_requirements: *12779320
+- !ruby/object:Gem::Dependency
+  name: rcov
+  requirement: &12778120 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *12778120
+description: Fasta reader, ORF emitter, sequence translation
+email: pjotr.public01@thebird.nl
+executables:
+- getorf
+- nt2aa.rb
+extensions: []
+extra_rdoc_files:
+- LICENSE
+- README.rdoc
+files:
+- Gemfile
+- Gemfile.lock
+- LICENSE
+- README.rdoc
+- Rakefile
+- VERSION
+- bin/getorf
+- bin/nt2aa.rb
+- bio-bigbio.gemspec
+- doc/bigbio_getorf.wtex
+- lib/bigbio.rb
+- lib/bigbio/adapters/translate.rb
+- lib/bigbio/db/blast.rb
+- lib/bigbio/db/blast/blastclust.rb
+- lib/bigbio/db/emitters/fasta_emitter.rb
+- lib/bigbio/db/emitters/orf_emitter.rb
+- lib/bigbio/db/fasta.rb
+- lib/bigbio/db/fasta/fastaindex.rb
+- lib/bigbio/db/fasta/fastapairedreader.rb
+- lib/bigbio/db/fasta/fastapairedwriter.rb
+- lib/bigbio/db/fasta/fastareader.rb
+- lib/bigbio/db/fasta/fastarecord.rb
+- lib/bigbio/db/fasta/fastawriter.rb
+- lib/bigbio/db/fasta/indexer.rb
+- lib/bigbio/environment.rb
+- lib/bigbio/sequence/predictorf.rb
+- lib/bigbio/sequence/translate.rb
+- spec/emitter_spec.rb
+- spec/predictorf_spec.rb
+- test/data/EMBOSS/EGC.1
+- test/data/fasta/nt.fa
+- test/doctest/test_fasta.rb
+- test/doctest/test_frames.rb
+- test/doctest/test_getorf.rb
+- test/doctest/test_paired.rb
+- test/performance/translate_with_biolib.rb
+- test/performance/translate_with_bioruby.rb
+homepage: http://github.com/pjotrp/bioruby-bigbioruby
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -3977311402144334707
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.10
+signing_key: 
+specification_version: 3
+summary: Low memory sequence emitters
+test_files:
+- spec/emitter_spec.rb
+- spec/predictorf_spec.rb
+- test/doctest/test_fasta.rb
+- test/doctest/test_frames.rb
+- test/doctest/test_getorf.rb
+- test/doctest/test_paired.rb
+- test/performance/translate_with_biolib.rb
+- test/performance/translate_with_bioruby.rb