transrate 1.0.0 → 1.0.1

data/lib/transrate/comparative_metrics.rb

@@ -36,6 +36,9 @@ module Transrate
     end
 
     def get_reference_hits crbblast
+      @reference.each do |name, contig|
+        contig.hits = []
+      end
       crbblast.reciprocals.each do |query_id, list|
         list.each do |hit|
           unless @reference.assembly.key? hit.target

data/lib/transrate/snap.rb

@@ -56,6 +56,7 @@ module Transrate
         runner = Cmd.new snapcmd
         runner.run
         save_readcount runner.stdout
+        save_logs(runner.stdout, runner.stderr)
         unless runner.status.success?
           if runner.stderr=~/Unmatched\sread\sIDs/
             logger.warn runner.stderr
@@ -71,6 +72,14 @@ module Transrate
       @bam
     end
 
+    def save_logs(stdout, stderr)
+      FileUtils.mkdir_p 'logs'
+      File.open('logs/snap.log', 'a') do |f|
+        f.write stdout
+        f.write stderr
+      end
+    end
+
     def remap_reads(left, right, threads)
       fixedleft = []
       fixedright = []
@@ -90,6 +99,7 @@ module Transrate
       runner = Cmd.new snapcmd
       runner.run
       save_readcount runner.stdout
+      save_logs(runner.stdout, runner.stderr)
       unless runner.status.success?
         raise SnapError.new("Snap failed\n#{runner.stderr}")
       end

data/lib/transrate/version.rb

@@ -10,7 +10,7 @@ module Transrate
   module VERSION
     MAJOR = 1
     MINOR = 0
-    PATCH = 0
+    PATCH = 1
     BUILD = nil
 
     STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')

data/packaging/build_deps_linux.sh

@@ -0,0 +1,57 @@
+export PATH=~/gcc-4.8.4/bin:~/cmake-3.1.3-Linux-x86_64/bin:$PATH
+
+cd ~
+
+# transrate-tools
+git clone --recursive https://github.com/Blahah/transrate-tools.git
+cd transrate-tools/bamtools
+mkdir build
+cd build
+cmake ..
+make
+cd ../..
+cmake .
+make
+## package it up
+cd src
+tar zcvf bam-read_v1.0.0.beta4_linux.tar.gz bam-read
+cp bam-read_v1.0.0.beta4_linux.tar.gz /vagrant/
+
+# snap
+git clone https://github.com/Blahah/snap.git
+cd snap
+git fetch
+git checkout dev
+make
+# package it up
+tar zcvf snap_v1.0dev.67.trfix1.tar.gz snap
+cp snap_v1.0dev.67.trfix1.tar.gz /vagrant/
+
+# salmon
+git clone https://github.com/kingsfordgroup/sailfish.git
+cd sailfish
+git fetch
+git checkout develop
+mkdir build
+cd build
+cmake -DFETCH_BOOST=TRUE -DCMAKE_INSTALL_PREFIX=~/sailfish/ ..
+make
+make install
+# collect libs for packaging
+cd ..
+scripts/cpld.bash bin/salmon lib
+rm lib/libc.so.6
+rm lib/ld-linux-x86-64l.so.2
+rm lib/libdl.so.2
+rm lib/libstdc++.so.6
+rm lib/libgcc_s.so.1
+rm lib/libpthread.so.0
+
+# package it up
+tar zcvf salmon_v0.3.0.tar.gz bin/salmon lib/
+cp salmon_v0.3.0.tar.gz /vagrant/
+
+# ruby 2.2 (for libruby)
+
+
+# transrate (for the c extension)

data/packaging/build_deps_macosx.sh

@@ -0,0 +1,55 @@
+brew tap homebrew/dupes
+brew tap homebrew/versions
+brew install cmake zlib gcc49 autoconf
+
+cd ~
+
+
+# transrate-tools
+git clone --recursive https://github.com/Blahah/transrate-tools.git
+## build bamtools
+cd transrate-tools/bamtools
+mkdir build
+cd build
+cmake ..
+make
+cd ../..
+## build transrate-tools, directly specifying the static LIBZ location
+cmake -DZLIB_LIBRARY=/usr/local/opt/zlib/lib/libz.a .
+make
+## package it up
+cd src
+tar zcvf bam-read_v1.0.0.beta4_osx.tar.gz bam-read
+cp bam-read_v1.0.0.beta4_osx.tar.gz /vagrant/
+
+
+# snap
+cd ~
+git clone https://github.com/Blahah/snap.git
+cd snap
+git fetch
+git checkout dev
+mv Makefile Makefile.old
+# make sure snap uses gcc
+sed 's/g\+\+/g\+\+-4\.9/g' Makefile.old > Makefile
+make
+# package it up
+tar zcvf snap_v1.0dev.67.trfix1.tar.gz snap
+cp snap_v1.0dev.67.trfix1.tar.gz /vagrant/
+
+
+# salmon
+git clone https://github.com/kingsfordgroup/sailfish.git
+cd sailfish
+git fetch
+git checkout develop
+mkdir build
+cd build
+cmake -DFETCH_BOOST=TRUE ..
+make
+make install
+cd ..
+# package it up
+install_name_tool -add_rpath ../lib bin/salmon
+tar zcvf salmon_v0.3.0.tar.gz bin/salmon lib/
+cp salmon_v0.3.0.tar.gz /vagrant/

data/packaging/bundler-config

@@ -0,0 +1,3 @@
+BUNDLE_PATH: .
+BUNDLE_WITHOUT: development
+BUNDLE_DISABLE_SHARED_GEMS: '1'

data/packaging/minify.sh

@@ -0,0 +1,43 @@
+#! /bin/sh
+
+# Remove tests
+rm -rf lib/app/ruby/*/gems/*/test
+rm -rf lib/app/ruby/*/gems/*/tests
+rm -rf lib/app/ruby/*/gems/*/spec
+rm -rf lib/app/ruby/*/gems/*/features
+rm -rf lib/app/ruby/*/gems/*/benchmark
+
+# Remove documentation
+rm -f lib/app/ruby/*/gems/*/README*
+rm -f lib/app/ruby/*/gems/*/CHANGE*
+rm -f lib/app/ruby/*/gems/*/Change*
+rm -f lib/app/ruby/*/gems/*/COPYING*
+rm -f lib/app/ruby/*/gems/*/LICENSE*
+rm -f lib/app/ruby/*/gems/*/MIT-LICENSE*
+rm -f lib/app/ruby/*/gems/*/*.txt
+rm -f lib/app/ruby/*/gems/*/*.md
+rm -f lib/app/ruby/*/gems/*/*.rdoc
+rm -rf lib/app/ruby/*/gems/*/doc
+rm -rf lib/app/ruby/*/gems/*/docs
+rm -rf lib/app/ruby/*/gems/*/example
+rm -rf lib/app/ruby/*/gems/*/examples
+rm -rf lib/app/ruby/*/gems/*/sample
+rm -rf lib/app/ruby/*/gems/*/doc-api
+find lib/app/ruby -name '*.md' | xargs rm -f
+
+# Remove misc unnecessary files
+rm -rf lib/app/ruby/*/gems/*/.gitignore
+rm -rf lib/app/ruby/*/gems/*/.travis.yml
+
+# Remove leftover native extension sources
+rm -f lib/app/ruby/*/gems/*/ext/Makefile
+rm -f lib/app/ruby/*/gems/*/ext/*/Makefile
+find lib/app/ruby -name '*.c' | xargs rm -f
+find lib/app/ruby -name '*.cpp' | xargs rm -f
+find lib/app/ruby -name '*.h' | xargs rm -f
+find lib/app/ruby -name '*.rl' | xargs rm -f
+find lib/app/ruby -name 'extconf.rb' | xargs rm -f
+
+# Remove Java files. They're only used for JRuby support
+find lib/app/ruby -name '*.java' | xargs rm -f
+find lib/app/ruby -name '*.class' | xargs rm -f

data/packaging/transrate

@@ -0,0 +1,20 @@
+#!/bin/bash
+set -e
+
+# Figure out where this script is located.
+SELFDIR="`dirname \"$0\"`"
+SELFDIR="`cd \"$SELFDIR\" && pwd`"
+
+# Temporarily set PATH and LD_LIBRARY_PATH
+export PATH=$SELFDIR/bin:$PATH
+export LD_LIBRARY_PATH=$SELFDIR/lib:$LD_LIBRARY_PATH
+export DYLD_FALLBACK_LIBRARY_PATH=$SELFDIR/lib:$DYLD_FALLBACK_LIBRARY_PATH
+# Tell Bundler where the Gemfile and gems are.
+export BUNDLE_GEMFILE="$SELFDIR/lib/app/Gemfile"
+unset BUNDLE_IGNORE_CONFIG
+
+# Tell transrate this is the packaged version
+export TRANSRATE_PACKAGED_BINARY=true
+
+# Run the actual app using the bundled Ruby interpreter, with Bundler activated.
+exec "$SELFDIR/lib/app/ruby/bin/ruby" -rbundler/setup "$SELFDIR/lib/app/bin/transrate" $@

data/test/data/test_contig_nc1.fa

@@ -0,0 +1,2 @@
+>contig1
+TTTCAGTTGATGAAGAAAAAACTAGAGTGTGTGGATTGCATGAAATGGGCTGGGGCTTGTTGGAATTTTGCTATTGAAACTAATGTTTACTTCAAATTGATAGGAATTCAGTTGGTTTTCTGGTGGTNTCTCTTTCTTCTTCACAATTGGATTTTGATTCCAAACACCATCTCTTGGGAATTCAGTTGGTTTTCTGGTGA

data/test/data/test_contig_nc2.fa

@@ -0,0 +1,4 @@
+>contig1
+GTTGATGAAGAAAAAACTAGAGTGTGTGGATTGCATGAAATGGGCTGGGGCTTGTTGGAATTTTGCTATTGAAACTAATGTTTACTTCAAATTGATAGGAATTCAGTTGGTTTTCTGGTGGTNTCTCTTTCTTCTTCACAATTGGATTTTGATTCCAAACACCATCTCTTGGGAATTCAGTTGGTTTTCTGGTGA
+>contig2
+TAGGAATTCAGTTGGTTTTCTGGTGGTNTCTCTTTCTTCTTCACAATTGGATTTTGATTCCAAACACCATCTCTTGGGAATTCAGTTGGTTTTCTGGTGATAAACACTTCAATTTGACTATGGACTCTGTGTATTGTAAAGAACATGATGACAGAATTGCTTCGAATCCGGTGGGTTTACAGTCATCCGGGTCGG

data/test/data/test_contig_nc3.fa

@@ -0,0 +1,6 @@
+>contig1
+TTTCAGTTGATGAAGAAAAAACTAGAGTGTGTGGATTGCATGAAATGGGCTGGGGCTTGTTGGAATTTTGCTATTGAAACTAATGTTTACTTCAAATTGA
+>contig2
+TAAACACTTCAATTTGACTATGGACTCTGTGTATTGTAAAGAACATGATGACAGAATTGCTTCGAATCCGGTGGGTTTACAGTCATCCGGGTCGGGTCCT
+>contig3
+TGGGGCTTGTTGGAATTTTGCTATTGAAACTAATGTTTACTTCAAATTGATAGGAATTCAGTTGGTTTTCTGGTGGTNTCTCTTTCTTCTTCACAATTGGATTTTGATTCCAAACACCATCTCTTGGGAATTCAGTTGGTTTTCTGGTGATAAACACTTCAATTTGACTATGGACTCTGTGTATTGTAAAGAACATGATG

data/test/data/test_contig_nc4.fa

@@ -0,0 +1,4 @@
+>contig1
+TGCATGAAATGGGCTGGGGCTTGTTGGAATTTTGCTATTGAAACTAATGTTTACTTCAAATTGATAGGAATTCAGTTGGTTTTCTGGTGGTNTCTCTTTCTTCTTCACAATTGGATTTTGATTCCAAACACCATCTCTTGGGAATTCAGT
+>contig2
+TGCATGAAATGGGCTGGGGCTTGTTGGAATTTTGCTATTGAAACTAATGTTTACTTCAAATTGATAGGAATTCAGTTGGTTTTCTGGTGGTNTCTCTTTCTTCTTCACAATTGGATTTTGATTCCAAACACCATCTCTTGGGAATTCAGT

data/test/data/test_contig_nc5.fa

@@ -0,0 +1,6 @@
+>contig1
+TGGGGCTTGTTGGAATTTTGCTATTGAAACTAATGTTTACTTCAAATTGATAGGAATTCAGTTGGTTTTCTGGTGGTNTCTCTTTCTTCTTCACAATTGGATTTTGATTCCAAACACCATCTCTTGGGAATTCAGTTGGTTTTCTGGTGATAAACACTTCAATTTGACTATGGACTCTGTGTATTGTAAAGAACATGATG
+>contig2
+TAGGAATTCAGTTGGTTTTCTGGTGGTNTCTCTTTCTTCTTCACAATTGGATTTTGATTCCAAACACCATCTCTTGGGAATTCAGTTGGTTTTCTGGTGA
+>contig3
+TTCAGTTGGTTTTCTGGTGGTNTCTCTTTCTTCTTCACAATTGGATTTTGATTCCAAACACCATCTCTTGGGAATTCAGTTGGTTTTCTGGTGATAAACA

data/test/data/test_contig_nc6.fa

@@ -0,0 +1,2 @@
+>contig1
+AGGAATTCAGTTGGTTTTCTGGTGGTNTCTCTTTCTTCTTCACAATTGGATTTTGATTCCAAACACCATCTCTTGGGAATTCAGTTGGTTTTCTGGTGAT

data/test/data/test_contig_nc7.fa

@@ -0,0 +1,2 @@
+>contig1
+GGAATTCAGTTGGTTTTCTGGTGGTNTCTCTTTCTTCTTCACAATTGGATTTTGATTCCAAACACCATCTCTTGGGAATTCAGTTGGTTTTCTGGTGATA

data/test/data/test_reference_aa1.fa

@@ -0,0 +1,2 @@
+>reference2
+FQLMKKKLECVDCMKWAGACWNFAIETNVYFKLIGIQLVFWWXLFLLHNWILIPNTISWEFSWFSGDKHFNLTMDSVYCKEHDDRIASNPVGLQSSGSGP

data/test/data/test_reference_nc1.fa

@@ -0,0 +1,2 @@
+>reference1
+TTTCAGTTGATGAAGAAAAAACTAGAGTGTGTGGATTGCATGAAATGGGCTGGGGCTTGTTGGAATTTTGCTATTGAAACTAATGTTTACTTCAAATTGATAGGAATTCAGTTGGTTTTCTGGTGGTNTCTCTTTCTTCTTCACAATTGGATTTTGATTCCAAACACCATCTCTTGGGAATTCAGTTGGTTTTCTGGTGATAAACACTTCAATTTGACTATGGACTCTGTGTATTGTAAAGAACATGATGACAGAATTGCTTCGAATCCGGTGGGTTTACAGTCATCCGGGTCGGGTCCT

data/test/helper.rb

@@ -7,13 +7,12 @@ SimpleCov.formatter = SimpleCov::Formatter::MultiFormatter[
 ]
 SimpleCov.start
 
+require "stringio"
+
 require 'minitest/autorun'
-begin
-  require 'turn/autorun'
-  Turn.config.format = :pretty
-  Turn.config.trace = 5
-rescue LoadError
-end
+require "minitest/reporters"
+Minitest::Reporters.use! Minitest::Reporters::SpecReporter.new
+
 require 'shoulda/context'
 require 'transrate'
 
@@ -29,3 +28,33 @@ test_files.each do |file|
     cmd.run
   end
 end
+
+def capture_stderr
+  real_stderr, $stderr = $stderr, StringIO.new
+  yield
+  $stderr.string
+ensure
+  $stderr = real_stderr
+end
+
+def capture_stdout
+  real_stdout, $stdout = $stdout, StringIO.new
+  yield
+  $stdout.string
+ensure
+  $stdout = real_stdout
+end
+
+# use within an at_exit block, exploits the capture of last exception in
+# the global var $!
+def last_exit_successful?
+  $!.nil? || $!.is_a?(SystemExit) && $!.success?
+end
+
+def sorghum_data
+  assembly = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.fa')
+  reference = File.join(File.dirname(__FILE__), 'data', 'Os.protein.2.fa')
+  left = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.1.fastq')
+  right = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.2.fastq')
+  [assembly, reference, left, right]
+end

data/test/test_assembly.rb

@@ -2,7 +2,7 @@ require 'helper'
 require 'bio'
 require 'tmpdir'
 
-class TestAssembly < Test::Unit::TestCase
+class TestAssembly < MiniTest::Test
 
   context "Assembly" do
 
@@ -41,8 +41,10 @@ class TestAssembly < Test::Unit::TestCase
           ref = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.fa')
           cmd = Transrate::Cmd.new("cat #{ref} #{ref} > tmp.fa")
           cmd.run
-          assert_raise Transrate::AssemblyError do
-            assembly = Transrate::Assembly.new("tmp.fa")
+          capture_stderr do
+            assert_raises Transrate::AssemblyError do
+              assembly = Transrate::Assembly.new("tmp.fa")
+            end
           end
         end
       end

data/test/test_cmd.rb

@@ -1,6 +1,6 @@
 require 'helper'
 
-class TestCmd < Test::Unit::TestCase
+class TestCmd < MiniTest::Test
 
   context "Cmd" do
 

data/test/test_cmdline.rb

@@ -0,0 +1,114 @@
+require 'helper'
+require 'csv'
+
+class TestCmdline < MiniTest::Test
+
+  context "Transrate" do
+
+    teardown do
+      `rm -rf transrate_results`
+    end
+
+    should "fail nicely on non existent assembly files" do
+      assert_raises Transrate::TransrateIOError do
+        Transrate::Cmdline.new("--assembly foo.fasta".split)
+      end
+    end
+
+    should "fail nicely when assembly is not provided" do
+      assert_raises Transrate::TransrateArgError do
+        Transrate::Cmdline.new("--left left.fq".split)
+      end
+    end
+
+    should "fail on non existent reference files" do
+      Dir.mktmpdir do |tmpdir|
+        Dir.chdir tmpdir do
+          assembly, reference, left, right = sorghum_data
+          assert_raises Transrate::TransrateIOError do
+            Transrate::Cmdline.new("--assembly #{assembly} --reference foo.fasta".split)
+          end
+        end
+      end
+    end
+
+    should "run on test data" do
+      Dir.mktmpdir do |tmpdir|
+        Dir.chdir tmpdir do
+          captured_stdout = capture_stdout do
+            assembly, reference, left, right = sorghum_data
+            cmd = "--assembly #{assembly}"
+            cmd << " --reference #{reference}"
+            cmd << " --left #{left}"
+            cmd << " --right #{right}"
+            c = Transrate::Cmdline.new(cmd.split)
+            c.run
+          end
+          assert File.exist?("transrate_results/assemblies.csv"), "csv file doesn't exist"
+          assert File.exist?("transrate_results/sorghum_100/contigs.csv"),
+                 "contig csv file doesn't exist"
+          hash = {}
+          CSV.foreach("transrate_results/assemblies.csv", :headers => true,
+                                       :header_converters => :symbol,
+                                       :converters => :all) do |row|
+            row.headers
+            row.fields
+            row.headers.zip(row.fields).each do |header, field|
+              hash[header]=field
+            end
+          end
+          assert_in_delta 137748, hash[:n_bases], 1000, "number of bases"
+          assert_equal 1692, hash[:n50], "n50"
+          assert_equal 2, hash[:n_refs_with_crbb], "number of crb hits"
+          assert_equal 2, hash[:n_contigs_with_crbb], "number of contigs with hits"
+        end
+      end
+    end
+
+    should "run on test data with comma separated list of fastq files" do
+      Dir.mktmpdir do |tmpdir|
+        Dir.chdir tmpdir do
+          captured_stdout = capture_stdout do
+            assembly, reference, left, right = sorghum_data
+            left = [left]
+            left << File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
+            right = [right]
+            right << File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
+            cmd = "--assembly #{assembly}"
+            cmd << " --left #{left.join(",")}"
+            cmd << " --right #{right.join(",")}"
+            c = Transrate::Cmdline.new(cmd.split)
+            c.run
+          end
+          assert File.exist?("transrate_results/assemblies.csv")
+          assert File.exist?("transrate_results/sorghum_100/contigs.csv"),
+                 "contig csv file doesn't exist"
+          hash = {}
+          CSV.foreach("transrate_results/assemblies.csv", :headers => true,
+                                       :header_converters => :symbol,
+                                       :converters => :all) do |row|
+            row.headers.zip(row.fields).each do |header, field|
+              hash[header]=field
+            end
+          end
+          assert_in_delta 137748, hash[:n_bases], 1000, "number of bases"
+          assert_equal 1692, hash[:n50], "n50"
+          assert_equal 25006 + 223, hash[:fragments], "number of reads"
+        end
+      end
+    end
+
+    should "fail when one of multiple assemblies is missing" do
+      assembly, reference, left, right = sorghum_data
+      assembly2 = "does_not_exist.fa"
+      cmd = " --assembly #{assembly},#{assembly2}"
+      cmd << " --reference #{reference}"
+      cmd << " --left #{left}"
+      cmd << " --right #{right}"
+      assert_raises Transrate::TransrateIOError do
+        Transrate::Cmdline.new(cmd.split)
+      end
+    end
+
+  end
+end