finishm 0.0.1 → 0.0.2

data/lib/assembly/graph_generator.rb

@@ -1,6 +1,5 @@
 require 'bio-velvet'
 require 'bio'
-require 'pry'
 
 class Bio::FinishM::GraphGenerator
   include Bio::FinishM::Logging

data/lib/assembly/probed_graph.rb

@@ -89,7 +89,6 @@ class Bio::FinishM::ProbedGraph
   # single ended then this method always returns []
   def paired_nodes(node)
     to_return_node_ids = Set.new
-    binding.pry
     log.debug "Found #{node.short_reads.length} short reads associated with node #{node}" if log.debug?
     node.short_reads.each do |read|
       pair_read_id = @velvet_sequences.pair_id(read.read_id)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: finishm
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
 platform: ruby
 authors:
 - Ben J. Woodcroft
@@ -14,104 +14,125 @@ dependencies:
   name: bio-ipcress
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.0'
 - !ruby/object:Gem::Dependency
   name: bio-logger
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.0'
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 1.4.3
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 1.4.3
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
 - !ruby/object:Gem::Dependency
   name: progressbar
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.21'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.21'
 - !ruby/object:Gem::Dependency
   name: bio-samtools
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.6'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.6'
 - !ruby/object:Gem::Dependency
   name: ruby-graphviz
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 1.0.9
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 1.0.9
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
 - !ruby/object:Gem::Dependency
   name: ds
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.0.4
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.0.4
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
 - !ruby/object:Gem::Dependency
   name: hopcsv
   requirement: !ruby/object:Gem::Requirement
     requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.4.3
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.4'
@@ -119,6 +140,9 @@ dependencies:
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.4.3
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.4'
@@ -156,42 +180,54 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 1.4.2
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 1.4.2
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
 - !ruby/object:Gem::Dependency
   name: yargraph
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.0.4
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.0.4
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.0'
 - !ruby/object:Gem::Dependency
-  name: files
+  name: pry
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.10'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.10'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -199,6 +235,9 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 2.8.0
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.8'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -206,32 +245,35 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 2.8.0
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.8'
 - !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
@@ -240,80 +282,59 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: 1.6.2
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: 1.6.2
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
 - !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:
-    - - ">="
+        version: 2.0.1
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '2.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 2.0.1
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
 - !ruby/object:Gem::Dependency
-  name: pry
+  name: bio-commandeer
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.1'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.1'
 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:
@@ -328,26 +349,7 @@ files:
 - 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
@@ -638,6 +640,7 @@ files:
 - ext/src/third-party/zlib-1.2.3/zutil.c
 - ext/src/third-party/zlib-1.2.3/zutil.h
 - ext/src/third-party/zlib-1.2.3/zutil.o
+- finishm.gemspec
 - lib/assembly/a_b_visualiser.rb
 - lib/assembly/acyclic_connection_finder.rb
 - lib/assembly/all_orfs.rb

data/bin/assembly_visualiser

@@ -1,106 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'optparse'
-require 'bio-logger'
-require 'bio-velvet'
-require 'graphviz'
-require 'bio'
-require 'set'
-
-SCRIPT_NAME = File.basename(__FILE__); LOG_NAME = 'finishm'
-$:.unshift File.join(File.dirname(__FILE__),'..','lib')
-require 'priner'
-
-# Parse command line options into the options hash
-options = {
-  :logger => 'stderr',
-  :log_level => 'info',
-  :start_kmers => [],
-  :end_kmers => [],
-  :coverage_cutoff => 0.0,
-}
-o = OptionParser.new do |opts|
-  opts.banner = "
-    Usage: #{SCRIPT_NAME} --velvet-graph PreGraphFile [options]
-
-    Take a graph pre-computed with velveth, and output a GraphViz file for visualisation.
-
-    Overlayed on top of this graph can be added information e.g. nodes that contain
-    particular kmers get coloured.
-    \n\n"
-
-  opts.on("--velvet-graph GRAPH_FILE", "PreGraph file output from velveth [required]") do |arg|
-    options[:velvet_pregraph_file] = arg
-  end
-
-  opts.separator "\nOptional arguments:\n\n"
-  opts.on("--dot OUTPUT_DOT_FILENAME", "Output the graph into PNG format [default: not output as DOT]") do |arg|
-    options[:dot_output_file] = arg
-  end
-  opts.on("--png OUTPUT_PNG_FILENAME", "Output the graph into PNG format [default: not output as PNG]") do |arg|
-    options[:neato_png] = arg
-  end
-  opts.on("--start-kmers-file FILE", "Path to file containing newline-separated kmers that are associated with the start of the assembly [default: none]") do |arg|
-    options[:start_kmers] = File.open(arg).read.split(/\s+/)
-  end
-  opts.on("--end-kmers-file FILE", "Path to file containing newline-separated kmers that are associated with the end of the assembly [default: none]") do |arg|
-    options[:end_kmers] = File.open(arg).read.split(/\s+/)
-  end
-  opts.on("--coverage-cutoff NUMBER", "Require at least this much coverage, otherwise the node and associated edges are not shown in the output [default: #{options[:coverage_cutoff]}]") do |arg|
-    options[:coverage_cutoff] = arg.to_f
-  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[:velvet_pregraph_file].nil?
-  $stderr.puts o
-  exit 1
-end
-if !(options[:dot_output_file] or options[:neato_png])
-  $stderr.puts "Need to specify an output format with e.g. --png or --dot"
-  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.info "Parsing graph from #{options[:velvet_pregraph_file]}"
-graph = Bio::Velvet::Graph.parse_from_file(options[:velvet_pregraph_file])
-log.info "Finished parsing graph, found #{graph.nodes.length} nodes and #{graph.arcs.length} arcs"
-
-if options[:start_kmers].length > 0
-  log.info "Read in #{options[:start_kmers].length} kmers associated with the start of the assembly"
-end
-if options[:end_kmers].length > 0
-  log.info "Read in #{options[:end_kmers].length} kmers associated with the end of the assembly"
-end
-list_of_start_kmers = options[:start_kmers].collect{|k| [k, Bio::Sequence::NA.new(k).reverse_complement.to_s]}.flatten
-list_of_end_kmers = options[:end_kmers].collect{|k| [k, Bio::Sequence::NA.new(k).reverse_complement.to_s]}.flatten
-
-if options[:coverage_cutoff]
-  cutter = Bio::AssemblyGraphAlgorithms::CoverageBasedGraphFilter.new
-  log.info "Removing low coverage (<#{options[:coverage_cutoff]}) nodes"
-  cutter.remove_low_coverage_nodes(graph, options[:coverage_cutoff])
-  log.info "After removing low coverage nodes, there is #{graph.nodes.length} nodes and #{graph.arcs.length} arcs"
-end
-
-viser = Bio::Assembly::ABVisualiser.new
-log.info "Converting assembly to GraphViz format"
-graphviz = viser.graphviz(graph, {:start_kmers => list_of_start_kmers, :end_kmers => list_of_end_kmers})
-
-# Print
-log.info "Printing assembly graph"
-if options[:dot_output_file]
-  graphviz.output :dot => options[:dot_output_file]
-end
-if options[:neato_png]
-  graphviz.output :png => options[:neato_png]
-end
-
-
-
-