bio-blastxmlparser 1.1.0 → 1.1.1

data/README.rdoc

@@ -28,10 +28,11 @@ see why libxml2 based Nokogiri is fast, see
 http://www.rubyinside.com/ruby-xml-performance-benchmarks-1641.html and
 http://www.xml.com/lpt/a/1703. 
 
-The parser is also designed with other optimizations, such as lazy evaluation,
-only creating objects when required, and (in a future version) parallelization. When parsing
-a full BLAST result usually only a few fields are used. By using XPath queries
-only the relevant fields are queried.
+The parser is also designed with other optimizations, such as lazy
+evaluation, i.e. only creating objects when required, and (in a future
+version) parallelization. When parsing a full BLAST result usually
+only a few fields are used. By using XPath queries only the relevant
+fields are queried.
 
 Timings for parsing test/data/nt_example_blastn.m7 (file size 3.4Mb) 
 
@@ -47,7 +48,7 @@ Timings for parsing test/data/nt_example_blastn.m7 (file size 3.4Mb)
   user    0m1.444s
   sys     0m0.160s
 
-  BioRuby ReXML DOM parser
+  BioRuby ReXML DOM parser (old style)
 
   real    1m14.548s
   user    1m13.065s
@@ -72,13 +73,88 @@ example on Debian:
 for more installation on other platforms see
 http://nokogiri.org/tutorials/installing_nokogiri.html. 
 
+== Command line usage
+
+=== Usage
+  blastxmlparser [options] file(s)
+
+    -p, --parser name                Use full|split parser (default full)
+        --output-fasta               Output FASTA
+    -n, --named fields               Set named fields
+    -e, --exec filter                Execute filter
+
+        --logger filename            Log to file (default stderr)
+        --trace options              Set log level (default INFO, see bio-logger)
+    -q, --quiet                      Run quietly
+    -v, --verbose                    Run verbosely
+        --debug                      Show debug messages
+    -h, --help                       Show help and examples
+
+  bioblastxmlparser filename(s)
+
+    Use --help switch for more information
+
+=== Examples
+
+Print result fields of iterations containing 'lcl', using a regex
+
+  blastxmlparser -e 'iter.query_id=~/lcl/' test/data/nt_example_blastn.m7
+
+Print fields where bit_score > 145
+
+  blastxmlparser -e 'hsp.bit_score>145' test/data/nt_example_blastn.m7
+
+prints a tab delimited
+
+  1       1       lcl|1_0 lcl|I_74685     1       5.82208e-34
+  2       1       lcl|1_0 lcl|I_1 1       5.82208e-34
+  3       2       lcl|2_0 lcl|I_2 1       6.05436e-59
+  4       3       lcl|3_0 lcl|I_3 1       2.03876e-56
+
+The second and third column show the BLAST iteration, and the others
+relate to the hits.
+
+As this is evaluated Ruby, it is also possible to use the XML element
+names directly
+
+  blastxmlparser -e 'hsp["Hsp_bit-score"].to_i>145' test/data/nt_example_blastn.m7
+
+And it is possible to print (non default) named fields where E-value < 0.001 
+and hit length > 100. E.g.
+
+  blastxmlparser -n 'hsp.evalue,hsp.qseq' -e 'hsp.evalue<0.01 and hit.len>100' test/data/nt_example_blastn.m7
+
+  1       5.82208e-34     AGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCT...
+  2       5.82208e-34     AGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCT...
+  3       2.76378e-11     AATATGGTAGCTACAGAAACGGTAGTACACTCTTC     
+  4       1.13373e-13     CTAAACACAGGAGCATATAGGTTGGCAGGCAGGCAAAAT 
+  5       2.76378e-11     GAAGAGTGTACTACCGTTTCTGTAGCTACCATATT     
+  etc. etc.
+
+prints the evalue and qseq columns. To output FASTA use --output-fasta
+
+  blastxmlparser --output-fasta -e 'hsp.evalue<0.01 and hit.len>100' test/data/nt_example_blastn.m7
+
+which prints matching sequences, where the first field is the accession, followed
+by query iteration id, and hit_id. E.g.
+
+  >I_74685 1|lcl|1_0 lcl|I_74685 [57809 - 57666] (REVERSE SENSE) 
+  AGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCTGCCTGCCAACCTATATGCTCCTGTGTTTAG
+  >I_1 1|lcl|1_0 lcl|I_1 [477 - 884] 
+  AGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCTGCCTGCCAACCTATATGCTCCTGTGTTTAG
+  etc. etc.
+
+To use the low-mem (iterated slower) version of the parser use
+
+  blastxmlparser --parser split -n 'hsp.evalue,hsp.qseq' -e 'hsp.evalue<0.01 and hit.len>100' test/data/nt_example_blastn.m7
+
 == API (Ruby library)
 
 To loop through a BLAST result:
 
     >> require 'bio-blastxmlparser'
     >> fn = 'test/data/nt_example_blastn.m7'
-    >>   n = Bio::Blast::XmlIterator.new(fn).to_enum
+    >>   n = Bio::BlastXMLParser::XmlIterator.new(fn).to_enum
     >>   n.each do | iter |
     >>     puts "Hits for " + iter.query_id
     >>     iter.each do | hit |
@@ -91,7 +167,7 @@ To loop through a BLAST result:
 The next example parses XML using less memory by using a Ruby
 Iterator
 
-    >> blast = Bio::Blast::XmlSplitterIterator.new(fn).to_enum
+    >> blast = Bio::BlastXMLParser::XmlSplitterIterator.new(fn).to_enum
     >> iter = blast.next
     >> iter.iter_num
     => 1
@@ -175,87 +251,11 @@ etc. etc.
 
 For more examples see the files in ./spec
 
-== Command line usage
-
-
-== Usage
-  blastxmlparser [options] file(s)
-
-    -p, --parser name                Use full|split parser (default full)
-        --output-fasta               Output FASTA
-    -n, --named fields               Set named fields
-    -e, --exec filter                Execute filter
-
-        --logger filename            Log to file (default stderr)
-        --trace options              Set log level (default INFO, see bio-logger)
-    -q, --quiet                      Run quietly
-    -v, --verbose                    Run verbosely
-        --debug                      Show debug messages
-    -h, --help                       Show help and examples
-
-  bioblastxmlparser filename(s)
-
-    Use --help switch for more information
-
-== Examples
-
-Print result fields of iterations containing 'lcl', using a regex
-
-  blastxmlparser -e 'iter.query_id=~/lcl/' test/data/nt_example_blastn.m7
-
-Print fields where bit_score > 145
-
-  blastxmlparser -e 'hsp.bit_score>145' test/data/nt_example_blastn.m7
-
-prints a tab delimited
-
-  1       1       lcl|1_0 lcl|I_74685     1       5.82208e-34
-  2       1       lcl|1_0 lcl|I_1 1       5.82208e-34
-  3       2       lcl|2_0 lcl|I_2 1       6.05436e-59
-  4       3       lcl|3_0 lcl|I_3 1       2.03876e-56
-
-The second and third column show the BLAST iteration, and the others
-relate to the hits.
-
-As this is evaluated Ruby, it is also possible to use the XML element
-names directly
-
-  blastxmlparser -e 'hsp["Hsp_bit-score"].to_i>145' test/data/nt_example_blastn.m7
-
-And it is possible to print (non default) named fields where E-value < 0.001 
-and hit length > 100. E.g.
-
-  blastxmlparser -n 'hsp.evalue,hsp.qseq' -e 'hsp.evalue<0.01 and hit.len>100' test/data/nt_example_blastn.m7
-
-  1       5.82208e-34     AGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCT...
-  2       5.82208e-34     AGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCT...
-  3       2.76378e-11     AATATGGTAGCTACAGAAACGGTAGTACACTCTTC     
-  4       1.13373e-13     CTAAACACAGGAGCATATAGGTTGGCAGGCAGGCAAAAT 
-  5       2.76378e-11     GAAGAGTGTACTACCGTTTCTGTAGCTACCATATT     
-  etc. etc.
-
-prints the evalue and qseq columns. To output FASTA use --output-fasta
-
-  blastxmlparser --output-fasta -e 'hsp.evalue<0.01 and hit.len>100' test/data/nt_example_blastn.m7
-
-which prints matching sequences, where the first field is the accession, followed
-by query iteration id, and hit_id. E.g.
-
-  >I_74685 1|lcl|1_0 lcl|I_74685 [57809 - 57666] (REVERSE SENSE) 
-  AGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCTGCCTGCCAACCTATATGCTCCTGTGTTTAG
-  >I_1 1|lcl|1_0 lcl|I_1 [477 - 884] 
-  AGTGAAGCTTCTAGATATTTGGCGGGTACCTCTAATTTTGCCTGCCTGCCAACCTATATGCTCCTGTGTTTAG
-  etc. etc.
-
-To use the low-mem (iterated slower) version of the parser use
-
-  blastxmlparser --parser split -n 'hsp.evalue,hsp.qseq' -e 'hsp.evalue<0.01 and hit.len>100' test/data/nt_example_blastn.m7
-
 == URL
 
 The project lives at http://github.com/pjotrp/blastxmlparser. If you use this software, please cite http://dx.doi.org/10.1093/bioinformatics/btq475
 
 == Copyright
 
-Copyright (c) 2011 Pjotr Prins under the MIT licence.  See LICENSE.txt and http://www.opensource.org/licenses/mit-license.html for further details.
+Copyright (c) 2011,2012 Pjotr Prins under the MIT licence.  See LICENSE.txt and http://www.opensource.org/licenses/mit-license.html for further details.
 

data/Rakefile

@@ -16,7 +16,7 @@ Jeweler::Tasks.new do |gem|
   gem.homepage = "http://github.com/pjotrp/blastxmlparser"
   gem.license = "MIT"
   gem.summary = %Q{Very fast BLAST XML parser and library for big data}
-  gem.description = %Q{Fast big data XML parser and library, libxml2 based 50x faster than BioRuby}
+  gem.description = %Q{Fast big data BLAST XML parser and library; this libxml2 based version is 50x faster than BioRuby}
   gem.email = "pjotr.public01@thebird.nl"
   gem.authors = ["Pjotr Prins"]
   # Include your dependencies below. Runtime dependencies are required when using your gem,

data/VERSION

@@ -1 +1 @@
-1.1.0
+1.1.1

data/bin/blastxmlparser

@@ -2,10 +2,9 @@
 #
 # BioRuby bio-blastxmlparser Plugin
 # Author:: Pjotr Prins
-# Copyright:: 2011
 # License:: MIT License
 #
-# Copyright (C) 2010,2011 Pjotr Prins <pjotr.prins@thebird.nl>
+# Copyright (C) 2010-2013 Pjotr Prins <pjotr.prins@thebird.nl>
 
 rootpath = File.dirname(File.dirname(__FILE__))
 $: << File.join(rootpath,'lib')
@@ -160,9 +159,9 @@ begin
   ARGV.each do | fn |
     logger.info("XML parsing #{fn}")
     n = if options.parser == :split
-      Bio::Blast::XmlSplitterIterator.new(fn).to_enum
+      Bio::BlastXMLParser::XmlSplitterIterator.new(fn).to_enum
     else
-      Bio::Blast::XmlIterator.new(fn).to_enum
+      Bio::BlastXMLParser::XmlIterator.new(fn).to_enum
     end
     i = 1
     n.each do | iter |

data/bio-blastxmlparser.gemspec

@@ -5,12 +5,12 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-blastxmlparser"
-  s.version = "1.1.0"
+  s.version = "1.1.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Pjotr Prins"]
-  s.date = "2012-08-08"
-  s.description = "Fast big data XML parser and library, libxml2 based 50x faster than BioRuby"
+  s.date = "2013-02-07"
+  s.description = "Fast big data BLAST XML parser and library; this libxml2 based version is 50x faster than BioRuby"
   s.email = "pjotr.public01@thebird.nl"
   s.executables = ["blastxmlparser"]
   s.extra_rdoc_files = [

data/lib/bio/db/blast/parser/nokogiri.rb

@@ -3,7 +3,7 @@ require 'nokogiri'
 require 'enumerator'
 
 module Bio
-  module Blast
+  module BlastXMLParser
 
     module XPath
       def field name

data/lib/bio/db/blast/xmliterator.rb

@@ -1,7 +1,7 @@
 
 
 module Bio
-  module Blast
+  module BlastXMLParser
 
     # Iterate a BLAST file yielding (lazy) results
     class XmlIterator

data/lib/bio/db/blast/xmlsplitter.rb

@@ -1,7 +1,7 @@
 require 'enumerator' 
 
 module Bio
-  module Blast
+  module BlastXMLParser
     # Reads a full XML result and splits it out into a buffer for each
     # Iteration (query result).
     class XmlSplitterIterator

data/sample/blastxmlparserdemo.rb

@@ -5,7 +5,7 @@ $: << File.join(rootpath,'lib')
 
 require 'bio-blastxmlparser'
 fn = 'test/data/nt_example_blastn.m7'
-n = Bio::Blast::XmlIterator.new(fn).to_enum
+n = Bio::BlastXMLParser::XmlIterator.new(fn).to_enum
 n.each do | iter |
   puts "Hits for " + iter.query_id
   iter.each do | hit |

data/spec/bio-blastxmlparser_spec.rb

@@ -1,9 +1,9 @@
 require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
 
 TESTFILE = "./test/data/nt_example_blastn.m7"
-include Bio::Blast
+include Bio::BlastXMLParser
 
-describe "Bio::Blast::NokogiriBlastXml" do
+describe "Bio::BlastXMLParser::NokogiriBlastXml" do
   before(:all) do
     n = NokogiriBlastXml.new(File.new(TESTFILE)).to_enum
     @iter1 = n.next
@@ -75,8 +75,8 @@ describe "Bio::Blast::NokogiriBlastXml" do
   end
 end
 
-describe Bio::Blast::XmlIterator do
-  include Bio::Blast
+describe Bio::BlastXMLParser::XmlIterator do
+  include Bio::BlastXMLParser
   it "should parse with Nokogiri" do
     blast = XmlIterator.new(TESTFILE).to_enum
     iter1 = blast.next
@@ -86,8 +86,8 @@ describe Bio::Blast::XmlIterator do
   end
 end
 
-describe Bio::Blast::XmlSplitterIterator do
-  include Bio::Blast
+describe Bio::BlastXMLParser::XmlSplitterIterator do
+  include Bio::BlastXMLParser
   # it "should read a large file and yield Iterations" do
   #   s = XmlSplitter.new("./test/data/nt_example_blastn.m7")
   #   s.each do | result |

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-blastxmlparser
 version: !ruby/object:Gem::Version
-  version: 1.1.0
+  version: 1.1.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-08-08 00:00:00.000000000Z
+date: 2013-02-07 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-logger
-  requirement: &14068420 !ruby/object:Gem::Requirement
+  requirement: &24214160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: 1.0.0
   type: :runtime
   prerelease: false
-  version_requirements: *14068420
+  version_requirements: *24214160
 - !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: &14067240 !ruby/object:Gem::Requirement
+  requirement: &24213120 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: 1.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *14067240
+  version_requirements: *24213120
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &14066000 !ruby/object:Gem::Requirement
+  requirement: &24212220 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: 0.9.2.2
   type: :development
   prerelease: false
-  version_requirements: *14066000
+  version_requirements: *24212220
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &14064760 !ruby/object:Gem::Requirement
+  requirement: &24211440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *14064760
+  version_requirements: *24211440
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &14063640 !ruby/object:Gem::Requirement
+  requirement: &24174660 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +65,10 @@ dependencies:
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: *14063640
+  version_requirements: *24174660
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &14062500 !ruby/object:Gem::Requirement
+  requirement: &24173840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,10 +76,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *14062500
+  version_requirements: *24173840
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &14055400 !ruby/object:Gem::Requirement
+  requirement: &24173100 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,8 +87,9 @@ dependencies:
         version: 2.4.2
   type: :development
   prerelease: false
-  version_requirements: *14055400
-description: Fast big data XML parser and library, libxml2 based 50x faster than BioRuby
+  version_requirements: *24173100
+description: Fast big data BLAST XML parser and library; this libxml2 based version
+  is 50x faster than BioRuby
 email: pjotr.public01@thebird.nl
 executables:
 - blastxmlparser
@@ -140,7 +141,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1696395694674995706
+      hash: -3287387609254152406
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: