intermine-bio 0.98.1

data/Gemfile

@@ -0,0 +1,4 @@
+source "http://rubygems.org"
+
+# Specify your gem's dependencies in intermine.gemspec
+gemspec

data/LICENCE

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
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data/README.rdoc

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+= Biological Extensions to the InterMine Webservice Client Library 
+
+This library is a set of extensions to the InterMine Webservices client, 
+providing access for data in biological formats. It directly extends the 
+InterMine classes, providing extra methods to the Query class.
+
+== Example
+
+Get all sequences for proteins on "h", "r", "eve", "bib" and "zen":
+
+    require "rubygems"
+    require "intermine/service"
+    require "intermine/bio"
+
+    s = Service.new("www.flymine.org/query")
+
+    puts s.query("Gene").select("proteins").where(:symbol => %w{h r eve bib zen}).fasta
+
+Process the locations of these genes one at a time:
+
+    s.query.select("Gene").where(:symbol => %w{h r eve bib zen}).bed do |line|
+      process line
+    end
+
+== Who is this for?
+
+InterMine data warehouses are typically constructed to hold
+Biological data, and as this library facilitates programmatic
+access to these data, this install is primarily aimed at 
+bioinformaticians. In particular, users of the following services
+may find it especially useful:
+ * FlyMine (http://www.flymine.org/query)
+ * YeastMine (http://yeastmine.yeastgenome.org/yeastmine)
+ * RatMine (http://ratmine.mcw.edu/ratmine)
+ * modMine (http://intermine.modencode.org/release-23)
+ * metabolicMine (http://www.metabolicmine.org/beta)
+
+These extensions are aimed at bioinformaticians looking to integrate
+these sources of data into other workflows.
+
+For details on constructing queries, see the intermine documentation.
+
+== Support
+
+Support is available on our development mailing list: dev@intermine.org
+
+== License
+
+This code is Open Source under the LGPL. Source code for all InterMine code
+can be checked out from svn://subversion.flymine.org/flymine

data/Rakefile

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+require 'rubygems'
+require 'rubygems/specification' unless defined?(Gem::Specification)
+require 'rake/testtask'
+require 'rake/gempackagetask'
+
+gem 'rdoc', '=2.1.0'
+require 'rdoc/rdoc'
+require 'rake/rdoctask'
+
+gem 'darkfish-rdoc'
+require 'darkfish-rdoc'
+
+def gemspec
+    @gemspec ||= begin
+        Gem::Specification.load(File.expand_path('intermine-bio.gemspec'))
+    end
+end
+
+task :default => :test
+
+desc 'Start a console session'
+task :console do
+    system 'irb -I lib -r rubygems -r intermine/service -r intermine/bio'
+end
+
+desc 'Displays the current version'
+task :version do 
+    puts "Current version: #{gemspec.version}"
+end
+
+desc 'Installs the gem locally'
+task :install => :package do
+    sh "gem install pkg/#{gemspec.name}-#{gemspec.version}"
+end
+
+desc 'Release the gem'
+task :release => :package do
+      sh "gem push pkg/#{gemspec.name}-#{gemspec.version}.gem"
+end
+
+Rake::GemPackageTask.new(gemspec) do |pkg|
+    pkg.need_zip = true
+    pkg.need_tar = true
+
+end
+
+Rake::TestTask.new do |t|
+    t.libs << "test"
+    t.test_files = FileList['test/unit_tests.rb']
+    t.verbose = true
+    t.warning = true
+end
+
+Rake::RDocTask.new do |t|
+    t.title = 'Bio Extensions to the InterMine Webservice Client'
+    t.rdoc_files.include 'README.rdoc'
+    t.rdoc_files.include 'lib/**/*rb'
+    t.main = 'README.rdoc'
+    t.options += ['-SHN', '-f', 'darkfish']
+end
+
+

data/contact_header.rdoc

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+#
+# [author] Alex Kalderimis dev@intermine.org
+# [homepage] http://www.intermine.org
+# [Licence] Copyright (C) 2002-2011 FlyMine
+# 
+#           This code may be freely distributed and modified under the
+#           terms of the GNU Lesser General Public Licence.  This should
+#           be distributed with the code.  See the LICENSE file for more
+#           information or http://www.gnu.org/copyleft/lesser.html.
+# 

data/lib/intermine/bio.rb

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+require "net/http"
+
+# == Biologically specific Extensions to the InterMine Data-Warehousing Webservices
+#
+# These modules provide interfaces to the biologically specific elements of the 
+# InterMine webservices. At present this consists of the ability to return results 
+# from queries in Biologically specific formats (GFF3, UCSC-BED, FASTA). The 
+# methods for accessing these formats provide mechanisms for iterating over the contents
+# in logical chunks.
+#
+#:include:contact_header.rdoc
+#
+module InterMine
+
+    # The Metadata for these extensions
+    #
+    #:include:contact_header.rdoc
+    #
+    module Bio
+
+        # The library version
+        VERSION = "0.98.1"
+        
+        # The library name
+        NAME = "intermine-bio"
+
+        # The project's homepage
+        HOMEPAGE = "http://www.intermine.org"
+
+        # The authors of this library
+        AUTHORS = ["Alex Kalderimis"]
+
+        # An email address to seek support at
+        EMAIL = ["dev@intermine.org"]
+    end
+
+    # Extensions to the PathQuery module.
+    #
+    #:include:contact_header.rdoc
+    #
+    module PathQuery
+
+        class BioError < RuntimeError
+        end
+
+        # Biologically specific Extensions to the Query class. 
+        #
+        # These methods provide mechanisms for accessing results in Biologically
+        # appropriate formats, being at present GFF3, FASTA, and UCSC-BED.
+        #
+        # The methods provided here can be used to both return the data as a string,
+        # and to iterate over the data in logical chunks, approriate to the format in question.
+        #
+        #:include:contact_header.rdoc
+        #
+        class Query
+
+            # Return the results from this query as GFF3
+            #
+            # If a block is given, each line of the GFF3 will be 
+            # yielded in turn, omitting any header lines, which are 
+            # returned at the end of the iteration, otherwise
+            # the content of the GFF3 results will be returned as one string.
+            #
+            #   header = query.gff3 do |line|
+            #      process line
+            #   end
+            #
+            #   puts query.gff3
+            #
+            def gff3
+                if block_given?
+                    header = ""
+                    results_reader.each_gff3 do |gff3|
+                        if gff3.start_with? "#"
+                            header << gff3
+                        else
+                            yield gff3
+                        end
+                    end
+                    return header
+                else
+                    buffer = ""
+                    results_reader.each_gff3 do |gff3|
+                        buffer.concat(gff3)
+                    end
+                    return buffer
+                end
+            end
+
+            # Return the results from this query as FASTA
+            #
+            # If a block is given, each FASTA record will be yielded
+            # in turn, and the query will be returned, otherwise
+            # the content of the FASTA results will be returned as one string.
+            #
+            #   query.fasta do |record|
+            #      process record
+            #   end
+            #
+            #   puts query.fasta
+            #
+            def fasta # :yields: record
+                if block_given?
+                    buffer = nil
+                    results_reader.each_fasta do |line|
+                        if line.start_with? ">"
+                            yield buffer unless buffer.nil?
+                            buffer = line
+                        else
+                            raise BioError, "Incorrect fasta - no header line" if buffer.nil?
+                            buffer << line
+                        end
+                    end
+                    yield buffer unless buffer.nil?
+                    return self
+                else
+                    buffer = ""
+                    results_reader.each_fasta do |line|
+                        buffer.concat(line)
+                    end
+                    return buffer
+                end
+            end
+
+            # Return the results from this query as BED
+            #
+            # If a block is given, each line of the BED results will be 
+            # yielded in turn, and the header will be returned, otherwise
+            # the content of the BED results will be returned as one string.
+            #
+            # If the optional parameter is set to false, then the "chr" prefix on
+            # the chromosome id will be omitted.
+            #
+            #   header = query.bed do |line|
+            #      process line
+            #   end
+            #
+            #   puts query.bed(false)
+            #
+            def bed(ucscCompatible=true)
+                if block_given?
+                    header = ""
+                    results_reader.each_bed(ucscCompatible) do |bed|
+                        if bed =~ /^\s*(#|track)/
+                            header << bed
+                        else
+                            yield bed
+                        end
+                    end
+                    return header
+                else
+                    buffer = ""
+                    results_reader.each_bed(ucscCompatible) do |bed|
+                        buffer.concat(bed)
+                    end
+                    return buffer
+                end
+            end
+        end
+    end
+
+    # Extensions to the Result processing code
+    #
+    #:include:contact_header.rdoc
+    #
+    module Results
+
+        # Extensions to the ResultsReader object
+        #
+        # These methods provide mechanisms for accessing the results in raw 
+        # format, and iterating over them line by line in a memory efficient
+        # manner. They are in no way content aware.
+        #
+        #:include:contact_header.rdoc
+        #
+        class ResultsReader
+
+            # The path to use to get the resource paths for the query variants
+            RESOURCE_PATH = "/check/"
+
+            # Yield results as GFF3
+            def each_gff3
+                adjust_path(:gff3)
+                each_line(params("gff3")) do |line|
+                    yield line
+                end
+            end
+
+            # Yield results as fasta
+            def each_fasta
+                adjust_path(:fasta)
+                each_line(params("fasta")) do |line|
+                    yield line
+                end
+            end
+
+            # Yield results as UCSC-BED
+            def each_bed(ucscCompatible=true)
+                adjust_path(:bed)
+                p = params("bed")
+                p["ucscCompatible"] = "no" unless ucscCompatible
+                each_line(p) do |line|
+                    yield line
+                end
+            end
+
+            # Adjust the path of this query to suit the currently selected format.
+            def adjust_path(variant)
+                @resources ||= {}
+                root = @query.service.root
+                uri = URI.parse(root + RESOURCE_PATH + "query." + variant.to_s)
+                @resources[variant] = Net::HTTP.get(uri.host, uri.path)
+                path = @resources[variant]
+                @uri = URI.parse(root + path)
+            end
+
+        end
+    end
+end
+

data/test/data/test.bed

@@ -0,0 +1,8 @@
+# UCSC BED format
+# Source: FlyMine
+# Genome Build: dm3
+track name=FlyMine_newtpreview_Custom_Track description="FlyMine newtpreview Custom Track" useScore=0
+chr2R   5866745 5868284 eve 0   +
+chr2R   5866745 5867058 eve:1   0   +
+chr2R   5866745 5868284 eve-RA  0   +
+chr2R   5867129 5868284 eve:2   0   +

data/test/data/test.fasta

@@ -0,0 +1,84 @@
+>ZEN1_DROME 362011840
+MSSVMHYYPVHQAKVGSYSADPSEVKYSDLIYGHHHDVNPIGLPPNYNQMNSNPTTLNDH
+CSPQHVHQQHVSSDENLPSQPNHDSQRVKLKRSRTAFTSVQLVELENEFKSNMYLYRTRR
+IEIAQRLSLCERQVKIWFQNRRMKFKKDIQGHREPKSNAKLAQPQAEQSAHRGIVKRLMS
+YSQDPREGTAAAEKRPMMAVAPVNPKPDYQASQKMKTEASTNNGMCSSADLSEILEHLAQ
+TTAAPQVSTATSSTGTSTNSASSSSSGHYSYNVDLVLQSIKQDLEAAAQAWSKSKSAPIL
+ATQSWHPSSQSQVPTSVHAAPSMNLSWGEPAAKSRKLSVNHMNPCVTSYNYPN
+>PYR1_DROME 362022982
+MASTDCYLALEDGTVLPGYSFGYVPSENESKVGFGGEVVFQTGMVGYTEALTDRSYSGQI
+LVLTYPLIGNYGVPAPDEDEHGLPLHFEWMKGVVQATALVVGEVAEEAFHWRKWKTLPDW
+LKQHKVPGIQDIDTRALTKKLREQGSMLGKIVYEKPPVEGLPKSSFVDPNVRNLAKECSV
+KERQVYGNPNGKGPRIAILDCGLKLNQLRCLLQRGASVTLLPWSARLEDEQFDALFLSNG
+PGNPESCDQIVQQVRKVIEEGQKPVFGICLGHQLLAKAIGCSTYKMKYGNRGHNLPCLHR
+ATGRCLMTSQNHGYAVDLEQLPDGWSELFVNANDGTNEGIVHASKPYFSVQFHPEHHAGP
+QDTEFLFDVFMESIQQKDLTIPQLIEQRLRPTTPAIDSAPVMPRKVLILGSGGLSIGQAG
+EFDYSGSQAIKAMRESNIQTVLINPNIATVQTSKGMADKCYFLPLTPHYVEQVIKSERPN
+GVLLTFGGQTALNCGVQLERAGVFSKYNVRILGTPIQSIIETEDRKLFAERVNEIGEQVA
+PSEAVYSVAQALDAASRLGYPVMARAAFSLGGLGSGFANNEEELQSLAQQALAHSSQLIV
+DKSLKGWKEVEYEVVRDAYNNCITVCNMENFDPLGIHTGESIVVAPSQTLSDREYQMLRS
+TALKVIRHFGVVGECNIQYALCPHSEQYYIIEVNARLSRSSALASKATGYPLAYVAAKLA
+LGLPLPDIKNSVTGNTTACFEPSLDYCVVKIPRWDLAKFVRVSKHIGSSMKSVGEVMAIG
+RNFEEAFQKALRMVDSDVLGFDPDVVPLNKEQLAEQLSEPTDRRPFVIAAALQLGMSLRE
+LHQLTNIDYWFLEKLERIILLQSLLTRNGSRTDAALLLKAKRFGFSDKQIAKYIKSTELA
+VRHQRQEFGIRPHVKQIDTVAGEWPASTNYLYHTYNGSEHDVDFPGGHTIVVGSGVYRIG
+SSVEFDWCAVGCLRELRKLQRPTIMINYNPETVSTDYDMCDRLYFEEISFEVVMDIYEME
+NSEGIILSMGGQLPNNIAMDLHRQQAKVLGTSPESIDCAENRFKFSRMLDRKGILQPRWK
+ELTNLQSAIEFCEEVGYPCLVRPSYVLSGAAMNVAYSNQDLETYLNAASEVSREHPVVIS
+KFLTEAKEIDVDAVASDGRILCMAVSEHVENAGVHSGDATLVTPPQDLNAETLEAIKRIT
+CDLASVLDVTGPFNMQLIAKNNELKVIECNVRVSRSFPFVSKTLDHDFVATATRAIVGLD
+VEPLDVLHGVGKVGVKVPQFSFSRLAGADVQLGVEMASTGEVACFGDNRYEAYLKAMMST
+GFQIPKNAVLLSIGSFKHKMELLPSIRDLAKMGYKLYASMGTGDFYAEHGVNVESVQWTF
+DKTTPDDINGELRHLAEFLANKQFDLVINLPMSGGGARRVSSFMTHGYRTRRLAVDYSIP
+LVTDVKCTKLLVESMRMNGGKPPMKTHTDCMTSRRIVKLPGFIDVHVHLREPGATHKEDF
+ASGTAAALAGGVTLVCAMPNTNPSIVDRETFTQFQELAKAGARCDYALYVGASDDNWAQV
+NELASHACGLKMYLNDTFGTLKLSDMTSWQRHLSHWPKRSPIVCHAERQSTAAVIMLAHL
+LDRSVHICHVARKEEIQLIRSAKEKGVKVTCEVCPHHLFLSTKDVERLGHGMSEVRPLLC
+SPEDQEALWENIDYIDVFATDHAPHTLAEKRSERPPPGFPGVETILPLLLQAVHEGRLTM
+EDIKRKFHRNPKIIFNLPDQAQTYVEVDLDEEWTITGNEMKSKSGWTPFEGTKVKGRVHR
+VVLRGEVAFVDGQVLVQPGFGQNVRPKQSPLASEASQDLLPSDNDANDTFTRLLTSEGPG
+GGVHGISTKVHFVDGANFLRPNSPSPRIRLDSASNTTLREYLQRTTNSNPVAHSLMGKHI
+LAVDMFNKDHLNDIFNLAQLLKLRGTKDRPVDELLPGKIMASVFYEVSTRTQCSFAAAML
+RLGGRVISMDNITSSVKKGESLEDSIKVVSSYADVVVLRHPSPGAVARAATFSRKPLINA
+GDGVGEHPTQALLDIFTIREEFGTVNGLTITMVGDLKNGRTVHSLARLLTLYNVNLQYVA
+PNSLQMPDEVVQFVHQRGVKQLFARDLKNVLPDTDVLYMTRIQRERFDNVEDYEKCCGHL
+VLTPEHMMRAKKRSIVLHPLPRLNEISREIDSDPRAAYFRQAEYGMYIRMALLAMVVGGR
+NTAL
+>FBpp0088674 362022983
+MASTDCYLALEDGTVLPGYSFGYVPSENESKVGFGGEVVFQTGMVGYTEALTDRSYSGQI
+LVLTYPLIGNYGVPAPDEDEHGLPLHFEWMKGVVQATALVVGEVAEEAFHWRKWKTLPDW
+LKQHKVPGIQDIDTRALTKKLREQGSMLGKIVYEKPPVEGLPKSSFVDPNVRNLAKECSV
+KERQVYGNPNGKGPRIAILDCGLKLNQLRCLLQRGASVTLLPWSARLEDEQFDALFLSNG
+PGNPESCDQIVQQVRKVIEEGQKPVFGICLGHQLLAKAIGCSTYKMKYGNRGHNLPCLHR
+ATGRCLMTSQNHGYAVDLEQLPDGWSELFVNANDGTNEGIVHASKPYFSVQFHPEHHAGP
+QDTEFLFDVFMESIQQKDLTIPQLIEQRLRPTTPAIDSAPVMPRKVLILGSGGLSIGQAG
+EFDYSGSQAIKAMRESNIQTVLINPNIATVQTSKGMADKCYFLPLTPHYVEQVIKSERPN
+GVLLTFGGQTALNCGVQLERAGVFSKYNVRILGTPIQSIIETEDRKLFAERVNEIGEQVA
+PSEAVYSVAQALDAASRLGYPVMARAAFSLGGLGSGFANNEEELQSLAQQALAHSSQLIV
+DKSLKGWKEVEYEVVRDAYNNCITVCNMENFDPLGIHTGESIVVAPSQTLSDREYQMLRS
+TALKVIRHFGVVGECNIQYALCPHSEQYYIIEVNARLSRSSALASKATGYPLAYVAAKLA
+LGLPLPDIKNSVTGNTTACFEPSLDYCVVKIPRWDLAKFVRVSKHIGSSMKSVGEVMAIG
+RNFEEAFQKALRMVDSDVLGFDPDVVPLNKEQLAEQLSEPTDRRPFVIAAALQLGMSLRE
+LHQLTNIDYWFLEKLERIILLQSLLTRNGSRTDAALLLKAKRFGFSDKQIAKYIKSTELA
+VRHQRQEFGIRPHVKQIDTVAGEWPASTNYLYHTYNGSEHDVDFPGGHTIVVGSGVYRIG
+SSVEFDWCAVGCLRELRKLQRPTIMINYNPETVSTDYDMCDRLYFEEISFEVVMDIYEME
+NSEGIILSMGGQLPNNIAMDLHRQQAKVLGTSPESIDCAENRFKFSRMLDRKGILQPRWK
+ELTNLQSAIEFCEEVGYPCLVRPSYVLSGAAMNVAYSNQDLETYLNAASEVSREHPVVIS
+KFLTEAKEIDVDAVASDGRILCMAVSEHVENAGVHSGDATLVTPPQDLNAETLEAIKRIT
+CDLASVLDVTGPFNMQLIAKNNELKVIECNVRVSRSFPFVSKTLDHDFVATATRAIVGLD
+VEPLDVLHGVGKVGVKVPQFSFSRLAGADVQLGVEMASTGEVACFGDNRYEAYLKAMMST
+GFQIPKNAVLLSIGSFKHKMELLPSIRDLAKMGYKLYASMGTGDFYAEHGVNVSIFMSVC
+LLYIMQL
+>BIB_DROME 362030490
+MADESLHTVPLEHNIDYHIVTLFERLEAMRKDSHGGGHGVNNRLSSTLQAPKRSMQAEIR
+TLEFWRSIISECLASFMYVFIVCGAAAGVGVGASVSSVLLATALASGLAMATLTQCFLHI
+SGAHINPAVTLALCVVRSISPIRAAMYITAQCGGGIAGAALLYGVTVPGYQGNLQAAISH
+SAALAAWERFGVEFILTFLVVLCYFVSTDPMKKFMGNSAASIGCAYSACCFVSMPYLNPA
+RSLGPSFVLNKWDSHWVYWFGPLVGGMASGLVYEYIFNSRNRNLRHNKGSIDNDSSSIHS
+EDELNYDMDMEKPNKYQQSQGTYPRGQSNGNGGGQAAGNGQHQAANMGQMPGVVANAGQG
+NYCQNLYTAPPLSSKYDQQQEPLYGGTRSLYCRSPTLTRSNLNRSQSVYAKSNTAINRDI
+VPRPGPLVPAQSLYPMRTQQQQQQQQQQQQQVAPAPQSSHLQNQNVQNQMQQRSESIYGM
+RGSMRGQQQPIQQQQQQQQQQQLQQQQPNMGVQQQQMQPPPQMMSDPQQQPQGFQPVYGT
+RTNPTPMDGNHKYDRRDPQQMYGVTGPRNRGQSAQSDDSSYGSYHGSAVTPPARHPSVEP
+SPPPPPMLMYAPPPQPNAAHPQPIRTQSERKVSAPVVVSQPAACAVTYTTSQGSAVTAQQ
+QQQQQQQQQQQQQQQQQQMMMQQQQQHYGMLPLRPN

data/test/data/test.gff3

@@ -0,0 +1,5 @@
+##gff-version 3
+2R      FlyMine gene    5866746 5868284 .       +       .       ID=FBgn0000606
+2R      FlyMine exon    5866746 5867058 .       +       .       ID=CG2328%3A1;Parent=FBgn0000606
+2R      FlyMine mRNA    5866746 5868284 .       +       .       ID=FBtr0088390;Parent=FBgn0000606
+2R      FlyMine exon    5867130 5868284 .       +       .       ID=CG2328%3A2;Parent=FBgn0000606

data/test/test_helper.rb

@@ -0,0 +1,67 @@
+$LOAD_PATH << File.expand_path( File.dirname(__FILE__) + '/../lib' )
+require "rexml/document"
+require "test/unit"
+
+include Test::Unit::Assertions
+
+def compare_xml(a, b)
+    require "rexml/document"
+    docA = REXML::Document.new(a.to_s)
+    docB = REXML::Document.new(b.to_s)
+
+    a_elems = docA.elements.to_a
+    b_elems = docB.elements.to_a
+
+    (0 ... a_elems.size).each do |idx|
+        compare_elements(a_elems[idx], b_elems[idx])
+    end
+end
+
+private
+
+def fail_xml_compare(elemA, elemB, problem, e)
+    formatter = REXML::Formatters::Pretty.new
+    elemA_str = String.new
+    elemB_str = String.new
+    formatter.write(elemA, elemA_str)
+    formatter.write(elemB, elemB_str)
+    first_part = "#{elemA_str}\nis not equal to\n#{elemB_str}\n"
+    
+    raise Test::Unit::AssertionFailedError, "#{first_part}because #{problem} - #{e.message}" 
+end
+
+def compare_elements(elemA, elemB)
+
+    begin
+        assert_equal(elemA.name, elemB.name)
+    rescue Test::Unit::AssertionFailedError => e
+        fail_xml_compare(elemA, elemB, "names of element differ", e)
+    end
+
+    begin
+        assert_equal(elemA.attributes, elemB.attributes)
+    rescue Test::Unit::AssertionFailedError => e
+        fail_xml_compare(elemA, elemB, "attributes of element differ", e)
+    end
+
+    begin
+        assert_equal(elemA.text, elemB.text)
+    rescue Test::Unit::AssertionFailedError => e
+        fail_xml_compare(elemA, elemB, "text contents of element differ", e)
+    end
+
+    begin
+        assert_equal(elemA.elements.size, elemB.elements.size)
+    rescue Test::Unit::AssertionFailedError => e
+        fail_xml_compare(elemA, elemB, "number of children of element differ", e)
+    end
+
+    a_elems = elemA.elements.to_a
+    b_elems = elemB.elements.to_a
+
+    (0 ... a_elems.size).each do |idx|
+        compare_elements(a_elems[idx], b_elems[idx])
+    end
+end
+
+

data/test/unit_tests.rb

@@ -0,0 +1,112 @@
+require File.dirname(__FILE__) + "/test_helper.rb"
+
+require "intermine/bio"
+require "test/unit"
+
+class MockQuery
+    def service
+        return MockService.new
+    end
+end
+
+class MockService
+    def root 
+        return "http://www.flymine.org/query/service"
+    end
+end
+
+module InterMine
+
+    module PathQuery
+
+        class Query
+
+            def results_reader
+                return InterMine::Results::ResultsReader.new(MockQuery.new)
+            end
+
+        end
+
+    end
+
+    module Results
+
+        class ResultsReader
+
+            attr_reader :uri
+
+            def initialize(mock_query)
+                @query = mock_query
+            end
+
+            def each_line(params)
+                f = File.new(File.dirname(__FILE__) + "/data/test.#{params[:format]}", "r")
+                f.each_line {|line| yield line}
+            end
+
+            def params(format)
+                return {:format => format}
+            end
+
+            unless ENV['LIVE_TESTING'] == "1"
+                def adjust_path(*args)
+                    # disable, as it makes requests
+                end
+            end
+
+        end
+    end
+end
+
+class TestBio < Test::Unit::TestCase
+
+    def setup
+        @rr = InterMine::Results::ResultsReader.new(MockQuery.new)
+    end
+
+    def testServiceResolution
+        if ENV['LIVE_TESTING'] == "1"
+            @rr.adjust_path("bed")
+            assert_equal("/query/service/query/results/bed", @rr.uri.path)
+            @rr.adjust_path("gff3")
+            assert_equal("/query/service/query/results/gff3", @rr.uri.path)
+            @rr.adjust_path("fasta")
+            assert_equal("/query/service/query/results/fasta", @rr.uri.path)
+        end
+    end
+
+    def testBedParsing
+        assert_equal(InterMine::PathQuery::Query.new.bed, File.new(File.dirname(__FILE__) + "/data/test.bed", "r").read)
+
+        c = 0
+        header = InterMine::PathQuery::Query.new.bed {|b| c += 1}
+        assert_equal(4, c)
+        assert_match(/Source: FlyMine/, header)
+    end
+
+    def testGff3Parsing
+        assert_equal(InterMine::PathQuery::Query.new.gff3, File.new(File.dirname(__FILE__) + "/data/test.gff3", "r").read)
+
+        c = 0
+        header = InterMine::PathQuery::Query.new.gff3 {|g| c += 1}
+        assert_equal(4, c)
+        assert_match(/gff-version 3/, header)
+    end
+
+    def testFastaParsing
+        assert_equal(InterMine::PathQuery::Query.new.fasta, File.new(File.dirname(__FILE__) + "/data/test.fasta", "r").read)
+
+        c = 0
+        last = nil
+        InterMine::PathQuery::Query.new.fasta {|f| c += 1; last = f}
+        assert_equal(4, c)
+        assert_match(/BIB_DROME 362030490/, last)
+    end
+
+end
+
+
+
+
+
+

metadata

@@ -0,0 +1,146 @@
+--- !ruby/object:Gem::Specification 
+name: intermine-bio
+version: !ruby/object:Gem::Version 
+  hash: 405
+  prerelease: false
+  segments: 
+  - 0
+  - 98
+  - 1
+  version: 0.98.1
+platform: ruby
+authors: 
+- Alex Kalderimis
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-08-02 00:00:00 +01:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: intermine
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id001
+description: |
+  = Biological Extensions to the InterMine Webservice Client Library 
+  
+  This library is a set of extensions to the InterMine Webservices client, 
+  providing access for data in biological formats. It directly extends the 
+  InterMine classes, providing extra methods to the Query class.
+  
+  == Example
+  
+  Get all sequences for proteins on "h", "r", "eve", "bib" and "zen":
+  
+      require "rubygems"
+      require "intermine/service"
+      require "intermine/bio"
+  
+      s = Service.new("www.flymine.org/query")
+  
+      puts s.query("Gene").select("proteins").where(:symbol => %w{h r eve bib zen}).fasta
+  
+  Process the locations of these genes one at a time:
+  
+      s.query.select("Gene").where(:symbol => %w{h r eve bib zen}).bed do |line|
+        process line
+      end
+  
+  == Who is this for?
+  
+  InterMine data warehouses are typically constructed to hold
+  Biological data, and as this library facilitates programmatic
+  access to these data, this install is primarily aimed at 
+  bioinformaticians. In particular, users of the following services
+  may find it especially useful:
+   * FlyMine (http://www.flymine.org/query)
+   * YeastMine (http://yeastmine.yeastgenome.org/yeastmine)
+   * RatMine (http://ratmine.mcw.edu/ratmine)
+   * modMine (http://intermine.modencode.org/release-23)
+   * metabolicMine (http://www.metabolicmine.org/beta)
+  
+  These extensions are aimed at bioinformaticians looking to integrate
+  these sources of data into other workflows.
+  
+  For details on constructing queries, see the intermine documentation.
+  
+  == Support
+  
+  Support is available on our development mailing list: dev@intermine.org
+  
+  == License
+  
+  This code is Open Source under the LGPL. Source code for all InterMine code
+  can be checked out from svn://subversion.flymine.org/flymine
+
+email: 
+- dev@intermine.org
+executables: []
+
+extensions: []
+
+extra_rdoc_files: []
+
+files: 
+- lib/intermine/bio.rb
+- test/data/test.bed
+- test/data/test.fasta
+- test/data/test.gff3
+- test/test_helper.rb
+- test/unit_tests.rb
+- LICENCE
+- Rakefile
+- README.rdoc
+- Gemfile
+- contact_header.rdoc
+has_rdoc: true
+homepage: http://www.intermine.org
+licenses: 
+- LGPL
+post_install_message: 
+rdoc_options: 
+- --title
+- Biological Extensions to the InterMine Webservice Client
+- --main
+- README.rdoc
+- --line-numbers
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: intermine-bio
+rubygems_version: 1.3.7
+signing_key: 
+specification_version: 3
+summary: Biological Extensions for the InterMine Webservice Client Library
+test_files: 
+- test/unit_tests.rb