finishm 0.0.1

data/spec/wander_spec.rb

@@ -0,0 +1,119 @@
+require 'tempfile'
+require 'bio'
+require 'bio-commandeer'
+require 'spec_helper'
+
+describe 'finishm wander' do
+  path_to_script = File.join(File.dirname(__FILE__),'..','bin','finishm wander')
+
+  it 'should scripting test ok with a 1 node thing' do
+    random = nil
+    Bio::FlatFile.foreach("#{TEST_DATA_DIR }/wander/1/random1.fa") do |s|
+      random = s.seq
+      break
+    end
+
+    Tempfile.open('testing') do |t|
+      #File.open('/tmp/contigs','w') do |t|
+      Tempfile.open('scaffolds') do |scaffs|
+        #File.open('/tmp/scaffolds','w') do |scaffs|
+        scaffs.close
+        t.puts '>first300'
+        t.puts random[0...300]
+        t.puts '>last400'
+        t.puts random[600..-1]
+        t.close
+        command = "#{path_to_script} --quiet --fasta #{TEST_DATA_DIR}/wander/1/random1.sammy.fa --contigs #{t.path} --output-connections /dev/stdout --overhang 100 --assembly-kmer 51 --output-scaffolds #{scaffs.path}"
+        output = Bio::Commandeer.run command
+        output.split("\n").should == [
+          "first300:end\tlast400:start\t399"
+          ]
+
+        scaffolds = []
+        Bio::FlatFile.foreach(scaffs.path){|s| scaffolds.push s}
+        scaffolds.collect{|s| s.definition}.should == %w(scaffold1)
+        scaffolds[0].seq.should == random[0...300] + 'N'*399 + random[600..-1]
+      end
+    end
+  end
+
+  it 'should work like scripting 1 node thing except calling it directly' do
+    random = nil
+    Bio::FlatFile.foreach("#{TEST_DATA_DIR }/wander/1/random1.fa") do |s|
+      random = s.seq
+      break
+    end
+
+    Tempfile.open('testing') do |t|
+      #File.open('/tmp/contigs','w') do |t|
+      t.puts '>first300'
+      t.puts random[0...300]
+      t.puts '>last400'
+      t.puts random[600..-1]
+      t.close
+
+      Tempfile.open('output_connections') do |conns|
+        conns.close
+
+        wanderer = Bio::FinishM::Wanderer.new
+        wanderer.run(Bio::FinishM::Wanderer::DEFAULT_OPTIONS.merge(
+          Bio::FinishM::GraphGenerator::DEFAULT_OPTIONS).merge({
+            :contigs_file => t.path,
+            :output_connection_file => conns.path,
+            :fasta_singles => "#{TEST_DATA_DIR}/wander/1/random1.sammy.fa",
+            :contig_end_length => 100,
+            }))
+      end
+    end
+  end
+
+  it 'should work with kmer recoherence' do
+    random = nil
+    Bio::FlatFile.foreach("#{TEST_DATA_DIR }/wander/1/random1.fa") do |s|
+      random = s.seq
+      break
+    end
+
+    Tempfile.open('testing') do |t|
+      #File.open('/tmp/contigs','w') do |t|
+      t.puts '>first300'
+      t.puts random[0...300]
+      t.puts '>last400'
+      t.puts random[600..-1]
+      t.close
+
+      Tempfile.open('output_connections') do |conns|
+        conns.close
+
+        wanderer = Bio::FinishM::Wanderer.new
+        wanderer.run(Bio::FinishM::Wanderer::DEFAULT_OPTIONS.merge(
+          Bio::FinishM::GraphGenerator::DEFAULT_OPTIONS).merge({
+            :contigs_file => t.path,
+            :output_connection_file => conns.path,
+            :fasta_singles => "#{TEST_DATA_DIR}/wander/1/random1.sammy.fa",
+            :contig_end_length => 100,
+            :recoherence_kmer => 71,
+            }))
+      end
+    end
+  end
+
+  it 'should croak when some seqs are too short' do
+    random = nil
+    Bio::FlatFile.foreach("#{TEST_DATA_DIR }/wander/1/random1.fa") do |s|
+      random = s.seq
+      break
+    end
+
+    Tempfile.open('testing') do |t|
+    #File.open('/tmp/contigs','w') do |t|
+      t.puts '>first50'
+      t.puts random[0...50]
+      t.puts '>last50'
+      t.puts random[random.length-50..-1]
+      t.close
+      command = "#{path_to_script} --quiet --fasta #{TEST_DATA_DIR}/wander/1/random1.sammy.fa --contigs #{t.path} --output-connections /dev/stdout --overhang 100 --assembly-kmer 51"
+      expect{Bio::Commandeer.run command}.to raise_error
+    end
+  end
+end

data/spec/watch_for_changes.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+DIRECTORY_TO_OBSERVE=`pwd`
+echo 'watching' $DIRECTORY_TO_OBSERVE
+function block_for_change {
+  inotifywait -r \
+    -e modify,move,create,delete \
+    $DIRECTORY_TO_OBSERVE
+}
+
+echo 'running' $1
+$1
+
+while block_for_change; do
+  echo 'running' $1
+  $1
+done

data/validation/fasta_compare.rb

@@ -0,0 +1,72 @@
+#!/usr/bin/env ruby
+
+require 'optparse'
+require 'bio-logger'
+require 'bio'
+
+SCRIPT_NAME = File.basename(__FILE__); LOG_NAME = SCRIPT_NAME.gsub('.rb','')
+
+# Parse command line options into the options hash
+options = {
+  :logger => 'stderr',
+  :log_level => 'info',
+}
+o = OptionParser.new do |opts|
+  opts.banner = "
+    Usage: #{SCRIPT_NAME} <arguments>
+
+Are the sequences in two files the same?\n\n"
+
+  opts.on("-1", "--fasta-1 FILE", "path to the first fasta file [required]") do |arg|
+    options[:first] = arg
+  end
+  opts.on("-2", "--fasta-2 FILE", "path to the second fasta file [required]") do |arg|
+    options[:second] = arg
+  end
+
+  # logger options
+  opts.separator "\nVerbosity:\n\n"
+  opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") {options[:log_level] = 'error'}
+  opts.on("--logger filename",String,"Log to file [default #{options[:logger]}]") { |name| options[:logger] = name}
+  opts.on("--trace options",String,"Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG"){|s| options[:log_level] = s}
+end; o.parse!
+if ARGV.length != 0 or options[:first].nil? or options[:second].nil?
+  $stderr.puts "More arguments required"
+  exit 1
+end
+# Setup logging
+Bio::Log::CLI.logger(options[:logger]); Bio::Log::CLI.trace(options[:log_level]); log = Bio::Log::LoggerPlus.new(LOG_NAME); Bio::Log::CLI.configure(LOG_NAME); log.outputters[0].formatter = Log4r::PatternFormatter.new(:pattern => "%5l %c %d: %m", :date_pattern => '%d/%m %T')
+
+
+#hash the first file
+firsts = {}
+Bio::FlatFile.foreach(options[:first]) do |seq|
+  name = seq.definition
+  raise "Duplicated seq name #{name}" if firsts.key?(name)
+
+  firsts[name] = seq.seq
+end
+
+sames = []
+differents = []
+Bio::FlatFile.foreach(options[:second]) do |seq|
+  name = seq.definition
+
+  unless firsts.key?(name)
+    raise "Unable to find sequence #{name} in the first file, when it exists in the second"
+  end
+  if firsts[name] == seq.seq
+    sames.push name
+  else
+    differents.push name
+  end
+end
+log.info "Found #{sames.length} sequences that were the same and #{differents.length} that were different"
+if log.debug?
+  sames.each do |same|
+    log.debug "#{same} was the same in each"
+  end
+  differents.each do |d|
+    log.debug "#{d} was different"
+  end
+end

data/validation/gapfill_simulate_perfect.rb

@@ -0,0 +1,108 @@
+#!/usr/bin/env ruby
+
+require 'optparse'
+require 'bio-logger'
+require 'bio'
+require 'bio-commandeer'
+require 'set'
+
+SCRIPT_NAME = File.basename(__FILE__); LOG_NAME = SCRIPT_NAME.gsub('.rb','')
+
+# Parse command line options into the options hash
+options = {
+  :max_gap_size => 1000,
+  :min_gap_size => 100,
+  :contig_end_buffer => 2000,
+  :num_to_gap => 100,
+
+  :logger => 'stderr',
+  :log_level => 'info',
+}
+o = OptionParser.new do |opts|
+  opts.banner = "
+    Usage: #{SCRIPT_NAME} <arguments>
+
+Introduce random gaps into sequences for the purpose of validating gap filling algorithms.\n\n"
+
+  opts.on("-i", "--input-fasta FILE", String, "Input fasta file of sequences for simulation [required]") do |arg|
+    options[:input_fasta_file] = arg
+  end
+  opts.on("--gapped FILE", String, "Output file with simulated gaps [required]") do |arg|
+    options[:gapped_output_file] = arg
+  end
+  opts.on("--answer FILE", String, "Output file with correct sequences, not including sequences that did not have gaps introduced [required]") do |arg|
+    options[:answer_output_file] = arg
+  end
+
+  opts.separator "\nOptional parameters:\n\n"
+  opts.on("--num-to-gap NUM", Integer, "Number of sequences to introduce gaps into [default: #{options[:num_to_gap]}]") do |arg|
+    options[:num_to_gap] = arg
+  end
+
+  # logger options
+  opts.separator "\nVerbosity:\n\n"
+  opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") {options[:log_level] = 'error'}
+  opts.on("--logger filename",String,"Log to file [default #{options[:logger]}]") { |name| options[:logger] = name}
+  opts.on("--trace options",String,"Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG"){|s| options[:log_level] = s}
+end; o.parse!
+if ARGV.length != 0
+  $stderr.puts o
+  exit 1
+end
+# Setup logging
+Bio::Log::CLI.logger(options[:logger]); Bio::Log::CLI.trace(options[:log_level]); log = Bio::Log::LoggerPlus.new(LOG_NAME); Bio::Log::CLI.configure(LOG_NAME); log.outputters[0].formatter = Log4r::PatternFormatter.new(:pattern => "%5l %c %d: %m", :date_pattern => '%d/%m %T')
+
+# Assumes that files to be simulated are >10kb in length
+# Count the number of sequences in the file with grep
+# choose 100 random ones to have gaps introduced artificially
+cmd = "cat #{options[:input_fasta_file]} |grep -c '>'"
+num_seqs = Bio::Commandeer.run cmd, :log => log
+num_seqs = num_seqs.to_i
+log.info "Found #{num_seqs} sequences in input file"
+raise "Input file problem - not enough seqs" if num_seqs < options[:num_to_gap]
+
+# Choose 100 random sequences, choosing indices
+indices_to_gap = Set.new ((0...num_seqs).to_a.sample(options[:num_to_gap]))
+
+# Read in fasta file into big hash, keeping only those sequences that have
+# been chosen randomly.
+i=0
+randomer = Random.new
+gapped_output = File.open(options[:gapped_output_file],'w')
+answer_output = File.open(options[:answer_output_file],'w')
+j=0
+Bio::FlatFile.foreach(options[:input_fasta_file]) do |seq|
+  if indices_to_gap.include?(i)
+    # introduce 100-1000bp gaps - choose length from uniform distribution
+    gap_size = randomer.rand(options[:max_gap_size]-options[:min_gap_size] )+options[:min_gap_size]
+    gap_size = gap_size.to_i
+
+    # ensure that the gap is more than 1kb away from the end of the sequence
+    seq_length = seq.seq.length
+    length_for_simulation = seq_length-2*options[:contig_end_buffer]-gap_size
+    raise "sequence length problem in #{seq.definition} - not long enough" unless length_for_simulation > 0
+    offset = randomer.rand(length_for_simulation).to_i
+
+    # log
+    name = ">#{j} #{seq.definition}"
+    log.info "Introducing a gap fo size #{gap_size} at position #{offset} into #{name}"
+
+    # Print out the gapped with introduced gaps
+    gapped_output.puts name
+    gapped_output.print seq.seq[0...offset]
+    gapped_output.print 'N'*gap_size
+    gapped_output.puts seq.seq[(offset+gap_size)..-1]
+
+    # Print out the answer without introduced gaps
+    answer_output.puts name
+    answer_output.puts seq.seq
+
+    j += 1
+  end
+  i += 1
+end
+
+gapped_output.close
+answer_output.close
+
+

metadata

@@ -0,0 +1,899 @@
+--- !ruby/object:Gem::Specification
+name: finishm
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Ben J. Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-07-30 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio-ipcress
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bio-logger
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: progressbar
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bio-samtools
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: ruby-graphviz
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: ds
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: hopcsv
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.4'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.4'
+- !ruby/object:Gem::Dependency
+  name: bio-velvet
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.6'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.6'
+- !ruby/object:Gem::Dependency
+  name: bio-velvet_underground
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.3'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.3'
+- !ruby/object:Gem::Dependency
+  name: ruby-progressbar
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: yargraph
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.0.4
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.0.4
+- !ruby/object:Gem::Dependency
+  name: files
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0.7'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bio-commandeer
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: De-novo assemblies generally only provide draft genomes. FinishM is aimed
+  at improving these draft assemblies.
+email: donttrustben near gmail.com
+executables:
+- assembly_visualiser
+- check_primer_combinations.rb
+- contig_joiner.rb
+- contigs_against_assembly.rb
+- finishm
+- finishm_assembler
+- finishm_gap_closer.rb
+- kmer_abundance_file_tool.rb
+- kmer_pattern_to_assembly.rb
+- kmer_profile_finder.rb
+- kmers_count_parse.d
+- kmers_count_tabulate.d
+- kmers_count_tabulate.rb
+- pcr_result_parser.rb
+- primer_finder.rb
+- read_selection_by_kmer.d
+- scaffold_by_pattern.rb
+- scaffold_connection_possibilities_to_knowns.rb
+- scaffold_end_coverages.rb
+- trail_validator.rb
+extensions:
+- ext/mkrf_conf.rb
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- ".document"
+- ".gitmodules"
+- ".rspec"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- bin/assembly_visualiser
+- bin/check_primer_combinations.rb
+- bin/contig_joiner.rb
+- bin/contigs_against_assembly.rb
+- bin/finishm
+- bin/finishm_assembler
+- bin/finishm_gap_closer.rb
+- bin/kmer_abundance_file_tool.rb
+- bin/kmer_pattern_to_assembly.rb
+- bin/kmer_profile_finder.rb
+- bin/kmers_count_parse.d
+- bin/kmers_count_tabulate.d
+- bin/kmers_count_tabulate.rb
+- bin/pcr_result_parser.rb
+- bin/primer_finder.rb
+- bin/read_selection_by_kmer.d
+- bin/scaffold_by_pattern.rb
+- bin/scaffold_connection_possibilities_to_knowns.rb
+- bin/scaffold_end_coverages.rb
+- bin/trail_validator.rb
+- ext/mkrf_conf.rb
+- ext/src/Makefile
+- ext/src/src/allocArray.c
+- ext/src/src/allocArray.h
+- ext/src/src/autoOpen.c
+- ext/src/src/autoOpen.h
+- ext/src/src/binarySequences.c
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+- spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.slightly_changed.fa
+- spec/data/assembly/1_simple_bubble_uneven_coverage/reads_combined.fa.gz
+- spec/data/assembly_visualiser/Contig_6_1_to_250.fa.kmers31
+- spec/data/assembly_visualiser/Contig_7_1_to_250.fa.kmers31
+- spec/data/assembly_visualiser/Graph
+- spec/data/assembly_visualiser/start_kmers1
+- spec/data/bands.csv
+- spec/data/c_probe_node_finder/1/CnyUnifiedSeq
+- spec/data/c_probe_node_finder/1/CnyUnifiedSeq.names
+- spec/data/c_probe_node_finder/1/Graph2
+- spec/data/c_probe_node_finder/1/LastGraph
+- spec/data/c_probe_node_finder/1/Log
+- spec/data/c_probe_node_finder/1/PreGraph
+- spec/data/c_probe_node_finder/1/Roadmaps
+- spec/data/c_probe_node_finder/1/contigs.fa
+- spec/data/c_probe_node_finder/1/stats.txt
+- spec/data/contig_printer/1/HOWTO_RECREATE
+- spec/data/contig_printer/1/contigs.fa
+- spec/data/contig_printer/1/seq.fa
+- spec/data/contig_printer/1/seq.fa.svg
+- spec/data/contig_printer/1/seq.fa.velvet/Graph2
+- spec/data/contig_printer/1/seq.fa.velvet/LastGraph
+- spec/data/contig_printer/1/seq.fa.velvet/Log
+- spec/data/contig_printer/1/seq.fa.velvet/PreGraph
+- spec/data/contig_printer/1/seq.fa.velvet/Roadmaps
+- spec/data/contig_printer/1/seq.fa.velvet/Sequences
+- spec/data/contig_printer/1/seq.fa.velvet/contigs.fa
+- spec/data/contig_printer/1/seq.fa.velvet/stats.txt
+- spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam
+- spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam.bai
+- spec/data/contig_printer/1/seq.node12.fa
+- spec/data/contig_printer/1/seq1_1to550.fa
+- spec/data/contig_printer/1/seq2_1to550.fa
+- spec/data/contig_printer/1/seq2_1to550.fa.fai
+- spec/data/explore/1/2seqs.sammy.fa
+- spec/data/explore/1/HOWTO_RECREATE.txt
+- spec/data/explore/1/a.fa
+- spec/data/explore/1/seq1_and_a.fa
+- spec/data/explore/1/seq2.fa
+- spec/data/fluff/1/2seqs.sammy.fa
+- spec/data/fluff/1/HOWTO_RECREATE.txt
+- spec/data/fluff/1/seq1.fa
+- spec/data/fluff/1/seq2.fa
+- spec/data/gapfilling/1/reads.fa
+- spec/data/gapfilling/1/trail_with_Ns.fa
+- spec/data/gapfilling/1/velvetAssembly/Graph2
+- spec/data/gapfilling/1/velvetAssembly/LastGraph
+- spec/data/gapfilling/1/velvetAssembly/Log
+- spec/data/gapfilling/1/velvetAssembly/PreGraph
+- spec/data/gapfilling/1/velvetAssembly/Roadmaps
+- spec/data/gapfilling/1/velvetAssembly/Sequences
+- spec/data/gapfilling/1/velvetAssembly/contigs.fa
+- spec/data/gapfilling/1/velvetAssembly/stats.txt
+- spec/data/gapfilling/2/HOWTO_recreate
+- spec/data/gapfilling/2/reference.fa
+- spec/data/gapfilling/2/reference_part1.fa
+- spec/data/gapfilling/2/reference_part2.fa
+- spec/data/gapfilling/2/sammy_reads.fa.gz
+- spec/data/gapfilling/2/with_gaps.fa
+- spec/data/gapfilling/3/HOWTO_recreate
+- spec/data/gapfilling/3/reads.fa.gz
+- spec/data/gapfilling/3/reference_part1.fa
+- spec/data/gapfilling/3/reference_part2.fa
+- spec/data/gapfilling/3/with_gaps.fa
+- spec/data/gapfilling/4/HOWTO_recreate
+- spec/data/gapfilling/4/reads.fa.gz
+- spec/data/gapfilling/5/HOWTO_RECREATE
+- spec/data/gapfilling/5/answer.fna
+- spec/data/gapfilling/5/gappy.fna
+- spec/data/gapfilling/5/reads.fa
+- spec/data/gapfilling/5/velvet51_3.5/LastGraph
+- spec/data/gapfilling/5/velvet51_3.5/Sequences
+- spec/data/gapfilling/6/random1.fa
+- spec/data/gapfilling/6/random2.fa
+- spec/data/gapfilling/6/random_sequence_length_2000
+- spec/data/gapfilling/6/reads.random1.fa.gz
+- spec/data/gapfilling/6/reads.random2.fa.gz
+- spec/data/gapfilling/6/to_gapfill.fa
+- spec/data/kmer_profile_to_assembly/multiple_abundance_file1.csv
+- spec/data/kmers_count1.csv
+- spec/data/kmers_count2.csv
+- spec/data/out
+- spec/data/positive_latching_pair.fa
+- spec/data/primers.csv
+- spec/data/read_selection_by_kmer/blacklist1.txt
+- spec/data/read_selection_by_kmer/input.fasta
+- spec/data/read_selection_by_kmer/whitelist1.txt
+- spec/data/read_selection_by_kmer/whitelist2.txt
+- spec/data/read_to_node/1_a_graph/HOWTO_RECREATE.txt
+- spec/data/read_to_node/1_a_graph/LastGraph
+- spec/data/read_to_node/1_a_graph/ReadToNode.bin
+- spec/data/read_to_node/2_no_read256_or_259/HOWTO_RECREATE.txt
+- spec/data/read_to_node/2_no_read256_or_259/LastGraph
+- spec/data/read_to_node/2_no_read256_or_259/ReadToNode.bin
+- spec/data/read_to_node/3_no_last_read/LastGraph
+- spec/data/read_to_node/3_no_last_read/ReadToNode.bin
+- spec/data/t/details.txt
+- spec/data/t/details.txt.srt
+- spec/data/t/location.txt
+- spec/data/t/location.txt.srt
+- spec/data/tweak/1_gap_then_unscaffolded/answer.fa
+- spec/data/tweak/1_gap_then_unscaffolded/reads.fa.gz
+- spec/data/tweak/1_gap_then_unscaffolded/scaffolds.fa
+- spec/data/tweak/2_second_genome/answer2.fa
+- spec/data/tweak/2_second_genome/reads.fa.gz
+- spec/data/tweak/3_variant/answer.fa
+- spec/data/tweak/3_variant/lesser_answer.fa
+- spec/data/tweak/3_variant/reads.fa.gz
+- spec/data/tweak/3_variant/with_gaps.fa
+- spec/data/velvet_test_trails/Assem/Graph
+- spec/data/velvet_test_trails/Assem/Graph2
+- spec/data/velvet_test_trails/Assem/LastGraph
+- spec/data/velvet_test_trails/Assem/Log
+- spec/data/velvet_test_trails/Assem/PreGraph
+- spec/data/velvet_test_trails/Assem/Roadmaps
+- spec/data/velvet_test_trails/Assem/Sequences
+- spec/data/velvet_test_trails/Assem/a.svg
+- spec/data/velvet_test_trails/Assem/contigs.fa
+- spec/data/velvet_test_trails/Assem/stats.txt
+- spec/data/velvet_test_trails/node_fwds.fa
+- spec/data/velvet_test_trails/node_seqs.fa
+- spec/data/velvet_test_trails/nodes_fwd_rev.fa
+- spec/data/velvet_test_trails/read1.fa
+- spec/data/velvet_test_trails/reads.fa
+- spec/data/velvet_test_trails_reverse/Assem/LastGraph
+- spec/data/velvet_test_trails_reverse/Assem/a.svg
+- spec/data/velvet_test_trails_reverse/reads_reversed.fa
+- spec/data/visualise/1/LastGraph
+- spec/data/visualise/2_paired_end/HOWTO_RECREATE.txt
+- spec/data/visualise/2_paired_end/rand1.fa
+- spec/data/visualise/2_paired_end/rand2.fa
+- spec/data/visualise/2_paired_end/with_gaps.fa
+- spec/data/visualise/2_paired_end/with_gaps.read_pairs.fa.gz
+- spec/data/wander/1/random1.fa
+- spec/data/wander/1/random1.sammy.fa
+- spec/depth_first_search_spec.rb
+- spec/dijkstra_spec.rb
+- spec/explore_spec.rb
+- spec/fluffer_spec.rb
+- spec/gapfiller_spec.rb
+- spec/graph_explorer_spec.rb
+- spec/graph_generator_spec.rb
+- spec/height_finder_spec.rb
+- spec/kmer_abundance_pattern_spec.rb
+- spec/kmer_coverage_based_path_filter_spec.rb
+- spec/kmer_profile_finder_spec.rb
+- spec/kmers_count_tabulate_spec.rb
+- spec/oriented_node_trail_spec.rb
+- spec/paired_end_neighbours_spec.rb
+- spec/paths_between_nodes_spec.rb
+- spec/priner_spec.rb
+- spec/read_input_spec.rb
+- spec/read_selection_by_kmer_spec.rb
+- spec/read_to_node_spec.rb
+- spec/roundup_spec.rb
+- spec/scaffold_breaker_spec.rb
+- spec/sequence_spec.rb
+- spec/single_coherent_paths_between_nodes_spec.rb
+- spec/single_coherent_wanderer_spec.rb
+- spec/single_ended_assembler_spec.rb
+- spec/spec_helper.rb
+- spec/velvet_graph_sequence_extractor_spec.rb
+- spec/visualise_spec.rb
+- spec/wander_spec.rb
+- spec/watch_for_changes.sh
+- validation/fasta_compare.rb
+- validation/gapfill_simulate_perfect.rb
+homepage: http://github.com/wwood/finishm
+licenses:
+- GPL
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: Genome improvement and finishing with or without further sequencing effort
+test_files: []