bio-ucsc-util 0.1.0

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.rvmrc

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+#!/usr/bin/env bash
+
+# This is an RVM Project .rvmrc file, used to automatically load the ruby
+# development environment upon cd'ing into the directory
+
+# First we specify our desired <ruby>[@<gemset>], the @gemset name is optional.
+environment_id="ruby-1.9.2-p290@ucsc-util"
+
+#
+# First we attempt to load the desired environment directly from the environment
+# file. This is very fast and efficient compared to running through the entire
+# CLI and selector. If you want feedback on which environment was used then
+# insert the word 'use' after --create as this triggers verbose mode.
+#
+if [[ -d "${rvm_path:-$HOME/.rvm}/environments" \
+  && -s "${rvm_path:-$HOME/.rvm}/environments/$environment_id" ]]
+then
+  \. "${rvm_path:-$HOME/.rvm}/environments/$environment_id"
+
+  if [[ -s "${rvm_path:-$HOME/.rvm}/hooks/after_use" ]]
+  then
+    . "${rvm_path:-$HOME/.rvm}/hooks/after_use"
+  fi
+else
+  # If the environment file has not yet been created, use the RVM CLI to select.
+  if ! rvm --create use  "$environment_id"
+  then
+    echo "Failed to create RVM environment ''."
+  fi
+fi
+
+#
+# If you use an RVM gemset file to install a list of gems (*.gems), you can have
+# it be automatically loaded. Uncomment the following and adjust the filename if
+# necessary.
+#
+# filename=".gems"
+# if [[ -s "$filename" ]] ; then
+#   rvm gemset import "$filename" | grep -v already | grep -v listed | grep -v complete | sed '/^$/d'
+# fi
+

data/Gemfile

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+source "http://rubygems.org"
+
+gem "ffi"
+
+group :test do
+  gem "shoulda", ">= 0"
+  gem 'shoulda-context'
+  gem "simplecov"
+end
+
+group :development do
+  gem "rdoc", "~> 3.12"
+  gem "bundler", "~> 1.0"
+  gem "jeweler", "~> 1.8.3"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    activesupport (3.2.6)
+      i18n (~> 0.6)
+      multi_json (~> 1.0)
+    ffi (1.1.0)
+    git (1.2.5)
+    i18n (0.6.0)
+    jeweler (1.8.4)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+      rdoc
+    json (1.7.3)
+    multi_json (1.3.6)
+    rake (0.9.2.2)
+    rdoc (3.12)
+      json (~> 1.4)
+    shoulda (3.1.1)
+      shoulda-context (~> 1.0)
+      shoulda-matchers (~> 1.2)
+    shoulda-context (1.0.0)
+    shoulda-matchers (1.2.0)
+      activesupport (>= 3.0.0)
+    simplecov (0.6.4)
+      multi_json (~> 1.0)
+      simplecov-html (~> 0.5.3)
+    simplecov-html (0.5.3)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.0)
+  ffi
+  jeweler (~> 1.8.3)
+  rdoc (~> 3.12)
+  shoulda
+  shoulda-context
+  simplecov

data/LICENSE.txt

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+Copyright (c) 2012 Nicholas A. Thrower
+
+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.rdoc

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+= bio-ucsc-util
+
+
+Ruby FFI binding and implementation of the ucsc utilities. The C source can be found here:
+http://hgdownload.cse.ucsc.edu/admin/
+
+More information about the ucsc genome browser data formats can be found here:
+http://genome.ucsc.edu/FAQ/FAQformat.html
+
+The following utilities are available
+
+- bedGraphToBigWig
+- wigToBigWig
+- bigWigInfo
+- bigWigSummary
+
+== Usage
+
+The Util class is used for the base conversion utilities:
+
+	Bio::Ucsc::Util.wigToBigWig('my.wig','chrom.sizes','out.bw')
+
+The BigWig class can be used to open and interact with the binary files:
+
+	bw = Bio::Ucsc::BigWig.open('out.bw')
+	bw.info
+	bw.summary('chr1',1,10,10,'mean')
+
+For more details see the Bio::Ucsc::Util and Bio::Ucsc::BigWig classes
+
+== Contributing to bio-ucsc-util
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.
+* Fork the project.
+* Start a feature/bugfix branch.
+* Commit and push until you are happy with your contribution.
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Dependencies
+
+* FFI (github.com/ffi/ffi)
+
+== Copyright
+
+Copyright (c) 2012 Nicholas A. Thrower. See LICENSE.txt for
+further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-ucsc-util"
+  gem.homepage = "http://github.com/throwern/bio-ucsc-util"
+  gem.license = "MIT"
+  gem.summary = %Q{Ruby binding to the ucsc kent utilities}
+  gem.description = %Q{Ruby FFI binding and implmentation of the ucsc utilities: bigWigInfo, bigWigSummary and wigToBigWig}
+  gem.email = "throwern@msu.edu"
+  gem.authors = ["throwern"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-ucsc-util #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/bio-ucsc-util.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "bio-ucsc-util"
+  s.version = "0.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["throwern"]
+  s.date = "2012-08-07"
+  s.description = "Ruby FFI binding and implmentation of the ucsc utilities: bigWigInfo, bigWigSummary and wigToBigWig"
+  s.email = "throwern@msu.edu"
+  s.extensions = ["ext/ucsc-util/mkrf_conf.rb"]
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    ".rvmrc",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bio-ucsc-util.gemspec",
+    "ext/ucsc-util/README",
+    "ext/ucsc-util/makefile",
+    "ext/ucsc-util/mkrf_conf.rb",
+    "ext/ucsc-util/ucsc-util-src-v268.tgz",
+    "lib/bio-ucsc-util.rb",
+    "lib/bio/ucsc/big_wig.rb",
+    "lib/bio/ucsc/binding.rb",
+    "lib/bio/ucsc/library.rb",
+    "lib/bio/ucsc/src/Version",
+    "lib/bio/ucsc/util.rb",
+    "test/1.bed",
+    "test/1.bw",
+    "test/1.wig",
+    "test/1_smoothed.bw",
+    "test/chrom.sizes",
+    "test/helper.rb",
+    "test/test_big_wig.rb"
+  ]
+  s.homepage = "http://github.com/throwern/bio-ucsc-util"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.24"
+  s.summary = "Ruby binding to the ucsc kent utilities"
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<ffi>, [">= 0"])
+      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
+    else
+      s.add_dependency(%q<ffi>, [">= 0"])
+      s.add_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_dependency(%q<bundler>, ["~> 1.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+    end
+  else
+    s.add_dependency(%q<ffi>, [">= 0"])
+    s.add_dependency(%q<rdoc>, ["~> 3.12"])
+    s.add_dependency(%q<bundler>, ["~> 1.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+  end
+end
+

data/ext/ucsc-util/README

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+This README was copied from the the jksrc.zip: kent/ directory. It contains the license stating
+src/lib, src/inc and src/utils directories are free for personal, academic, and commercial use.
+These folders have been extracted into an archive for use by this rubygem. 
+
+The data was retrieved from:
+http://hgdownload.cse.ucsc.edu/admin/jksrc.v268.zip
+
+3 of the original source files have modified code that relies on static (private) methods. New versions need to incorporate these changes.
+See bigWigSmooth in:
+-inc/bwgInternal.h
+-inc/bigWig.h
+-lib/bwgCreate.c
+
+Also converted **environ calls to support OSX shared library in cheapcgi.h/c
+#if defined __environ
+    extern char **environ;
+    INLINE char **getEnviron() {return environ;}
+#else
+    #include <crt_externs.h>
+    INLINE char **getEnviron() { return (*_NSGetEnviron()); }
+#endif
+
+---Original README below
+
+CONTENTS AND COPYRIGHT
+
+This directory contains the entire source tree for the
+UCSC Genome Bioinformatics Group's suite of biological analysis 
+and web display programs as well as some of Jim Kent's own tools.  
+All files are copyrighted, but license is hereby granted for personal, 
+academic, and non-profit use.  A license is also granted for the contents 
+of the src/lib, src/inc and src/utils and python directories for commercial 
+users.  Commercial users should contact kent@soe.ucsc.edu for access to other 
+modules.  Commercial users interested in the UCSC Genome Browser in particular 
+please see
+    http://genome.ucsc.edu/license/.
+
+Most source code users will only be interested in the src/inc and 
+src/lib directories, which contain the interfaces and implementations
+to the library routines,  and in a few specific applications.
+The applications are scattered in other directories.  Many of them are web based.  
+The UCSC Genome Browser in particular is mostly found in src/hg/hgTracks.
+
+GENERAL INSTALL INSTRUCTIONS
+
+1. Get the code.  The best way to do this now for
+   Unix users is via Git following the instructions at:
+     http://genome.ucsc.edu/admin/git.html
+   Or, fetch the entire source in a single file:
+     http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
+   Note further documentation for the build process in your
+   unpacked source tree in src/product/README.*
+   Especially note README.building.source and the "Known problems"
+   for typical situations you may encounter.
+2. Check that the environment variable MACHTYPE
+   exists on your system.  It should exist on Unix/Linux.  
+   (And making this on non-Unix systems is beyond
+   the scope of this README).  The default MACHTYPE is often a
+   long string: "i386-redhat-linux-gnu"
+   which will not function correctly in this build environment.
+   It needs to be something simple such as one of:
+	i386 i686 sparc alpha x86_64 ppc etc ...
+   with no other alpha characters such as: -
+   To determine what your system reports itself as, try the
+   uname options:  'uname -m' or 'uname -p' or 'uname -a'
+   on your command line.  If necessary set this environment variable.
+   Do this under the bash shell as so:
+       MACHTYPE=something
+       export MACHTYPE
+   or under tcsh as so:
+       setenv MACHTYPE something
+   and place this setting in your home directory .bashrc or .tcshrc
+   environment files so it will be set properly the next time you
+   login.  Remember to "export" it as show here for the bash shell.
+3. Make the directory ~/bin/$MACHTYPE which is
+   where the (non-web) executables will go.
+   Add this directory to your path.
+4. Go to the src/lib directory.  If it doesn't
+   already exist do a mkdir $MACHTYPE.
+5. Type make.  On Alphas there will be 
+   some warning messages about "crudeAli.c"
+   otherwise it should compile cleanly.
+   It's using gcc.
+6. Go to src/jkOwnLib and type make.
+7. Go to the application you want to make and type 
+   make.  (If you're not sure, as a simple test
+   go to src/utils/fixcr and type make,
+   then 'rehash' if necessary so your shell
+   can find the fixcr program in ~/bin/$(MACHTYPE).
+   The fixcr program changes Microsoft style
+   <CR><LF> line terminations to Unix style
+   <LF> terminations.  Look at the "gotCr.c"
+   file in the fixCr directory, and then
+   do a "fixcr gotCr.c" on it.
+
+
+INSTALL INSTRUCTIONS FOR BLAT
+
+1. Follow the general install instructions above.
+2. If you're on an alpha system do a:
+     setenv SOCKETLIB -lxnet
+   on Solaris do
+     setenv SOCKETLIB "-lsocket -lnsl"
+   on SunOS do
+     setenv SOCKETLIB "-lsocket -lnsl -lresolv"
+   on Linux you can skip this step.
+3. Execute make in each of the following directories:
+     src/gfServer
+     src/gfClient
+     src/blat
+     src/utils/faToNib
+
+INSTALL INSTRUCTIONS FOR CODE USING THE BROWSER DATABASE
+(and other code in the src/hg subdirectory)
+
+1. Follow the general install instructions above.
+2. Make the environment variable MYSQLINC point to
+   where MySQL's include files are.  (On my
+   system they are at /usr/include/mysql.)
+   While you're at it set the MYSQLLIBS
+   variable to point to something like
+   /usr/lib/mysql/libmysqlclient.a -lz
+   When available, the commands: mysql_config --include
+	and mysql_config --libs
+	will display the required arguments for these environment settings.
+3. Execute make in src/hg/lib
+4. Execute make in the directory containing the
+   application you wish to build.
+5. See also: http://genome.ucsc.edu/admin/jk-install.html
+   and more documentation in this source tree about setting up
+   a working browser in README files:
+       src/product/README.building.source
+       src/product/README.local.git.source
+       src/product/README.mysql.setup
+       src/product/README.install
+       src/product/README.trackDb
+       src/hg/makeDb/trackDb/README
+   There are numerous README files in the source tree describing
+   functions or modules in that area of the source tree.
+   The src/README in particular should be read by anyone modifying
+   the C source code, and python/README by anyone modifying the Python.
+

data/ext/ucsc-util/makefile

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+include ../inc/common.mk
+L += ${SOCKETLIB} -lm -lz
+
+O = aliType.o annoColumn.o annoFilter.o annoFormatter.o annoFormatTab.o \
+    annoGrator.o annoGratorQuery.o annoOption.o annoRow.o annoStreamer.o annoStreamVcf.o \
+    apacheLog.o asParse.o axt.o axtAffine.o bamFile.o base64.o \
+    basicBed.o bbiRead.o bbiWrite.o bigBed.o binRange.o bits.o \
+    blastOut.o blastParse.o boxClump.o boxLump.o bPlusTree.o \
+    bwgCreate.o bwgQuery.o bwgValsOnChrom.o \
+    cda.o chain.o chainBlock.o chainConnect.o chainToAxt.o chainToPsl.o \
+    cheapcgi.o cirTree.o codebias.o colHash.o common.o correlate.o crTree.o \
+    dgRange.o diGraph.o dlist.o dnaLoad.o dnaMarkov.o dnaMotif.o dnaseq.o \
+    dnautil.o dtdParse.o dystring.o \
+    emblParse.o errCatch.o errabort.o \
+    fa.o ffAli.o ffScore.o filePath.o fixColor.o flydna.o fof.o \
+    font/mgCourier10.o font/mgCourier12.o font/mgCourier14.o font/mgCourier18.o \
+    font/mgCourier24.o font/mgCourier34.o font/mgCourier8.o font/mgHelvetica10.o \
+    font/mgHelvetica12.o font/mgHelvetica14.o font/mgHelvetica18.o font/mgHelvetica24.o \
+    font/mgHelvetica34.o font/mgHelvetica8.o font/mgHelveticaBold10.o font/mgHelveticaBold12.o \
+    font/mgHelveticaBold14.o font/mgHelveticaBold18.o font/mgHelveticaBold24.o \
+    font/mgHelveticaBold34.o font/mgHelveticaBold8.o font/mgSixhi6.o font/mgSail8.o \
+    font/mgTimes10.o font/mgTimes12.o font/mgTimes14.o font/mgTimes18.o \
+    font/mgTimes24.o font/mgTimes34.o font/mgTimes8.o font/mgMenlo12.o \
+    fuzzyShow.o \
+    gapCalc.o gdf.o gemfont.o genomeRangeTree.o \
+    gfNet.o gff.o gff3.o gfxPoly.o gifLabel.o \
+    hacTree.o hash.o histogram.o hmmPfamParse.o hmmstats.o htmlPage.o htmshell.o \
+    https.o intExp.o intValTree.o internet.o itsa.o iupac.o \
+    jointalign.o jpegSize.o keys.o knetUdc.o kxTok.o linefile.o lineFileOnBigBed.o localmem.o log.o \
+    maf.o mafFromAxt.o mafScore.o memalloc.o memgfx.o metaWig.o mgCircle.o \
+    mgPolygon.o mime.o net.o nib.o nibTwo.o nt4.o numObscure.o \
+    obscure.o oldGff.o oligoTm.o options.o osunix.o pairHmm.o peakCluster.o \
+    phyloTree.o pipeline.o portimpl.o pngwrite.o psGfx.o psPoly.o pscmGfx.o \
+    psl.o pslGenoShow.o pslShow.o pslTbl.o pslTransMap.o pthreadWrap.o \
+    qa.o quickHeap.o quotedP.o \
+    ra.o rainbow.o rbTree.o rangeTree.o regexHelper.o repMask.o \
+    rle.o rnautil.o rqlEval.o rqlParse.o rudp.o \
+    scoreWindow.o seg.o seqOut.o seqStats.o servBrcMcw.o servCrunx.o \
+    servcis.o servcl.o servmsII.o servpws.o shaRes.o slog.o snof.o \
+    snofmake.o snofsig.o spaceSaver.o spacedColumn.o spacedSeed.o \
+    splatAli.o sqlList.o sqlNum.o subText.o sufa.o sufx.o synQueue.o \
+    tabRow.o textOut.o tokenizer.o trix.o twoBit.o \
+    udc.o vcf.o vGfx.o vPng.o verbose.o \
+    wildcmp.o wormdna.o \
+    xAli.o xa.o xap.o xenshow.o xmlEscape.o xp.o zlibFace.o
+
+vpath %.c ../utils/bedGraphToBigWig/
+
+XO = bedGraphToBigWig.o
+
+lib: libucsc.a
+	
+libucsc.a: $(O)
+	ar rcus $@ $(O)
+
+libucsc.so.1:$(O) $(XO)
+	$(CC) -shared -Wl,-soname,libucsc.so -pthread $(L) -o $@ $(O) $(XO) -lc 
+
+libucsc.1.dylib:$(O) $(XO)
+	libtool -dynamic -L/usr/X11/lib/ -g -lpthread $(L) -lc $(O) $(XO) -o $@
+	
+clean:
+	rm -f ${O} $(XO) libucsc.a
+
+tags:
+	etags ../inc/*.h ../lib/*.h ../lib/*.c