finishm 0.0.1
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- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
- data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
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- data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
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- data/lib/assembly/a_b_visualiser.rb +169 -0
- data/lib/assembly/acyclic_connection_finder.rb +81 -0
- data/lib/assembly/all_orfs.rb +615 -0
- data/lib/assembly/bad_format_writer.rb +46 -0
- data/lib/assembly/bam_probe_read_selector.rb +48 -0
- data/lib/assembly/bubbly_assembler.rb +842 -0
- data/lib/assembly/c_probe_node_finder.rb +38 -0
- data/lib/assembly/connection_interpreter.rb +350 -0
- data/lib/assembly/contig_printer.rb +400 -0
- data/lib/assembly/coverage_based_graph_filter.rb +68 -0
- data/lib/assembly/depth_first_search.rb +63 -0
- data/lib/assembly/dijkstra.rb +216 -0
- data/lib/assembly/fluffer.rb +253 -0
- data/lib/assembly/graph_explorer.rb +85 -0
- data/lib/assembly/graph_generator.rb +315 -0
- data/lib/assembly/height_finder.rb +355 -0
- data/lib/assembly/hybrid_velvet_graph.rb +70 -0
- data/lib/assembly/input_genome.rb +182 -0
- data/lib/assembly/kmer_coverage_based_path_filter.rb +65 -0
- data/lib/assembly/node_finder.rb +171 -0
- data/lib/assembly/oriented_node_trail.rb +507 -0
- data/lib/assembly/paired_end_assembler.rb +53 -0
- data/lib/assembly/paired_end_neighbour_finder.rb +176 -0
- data/lib/assembly/probed_graph.rb +105 -0
- data/lib/assembly/read_input.rb +79 -0
- data/lib/assembly/read_to_node.rb +37 -0
- data/lib/assembly/scaffold_breaker.rb +126 -0
- data/lib/assembly/sequence_hasher.rb +71 -0
- data/lib/assembly/single_coherent_paths_between_nodes.rb +533 -0
- data/lib/assembly/single_coherent_wanderer.rb +261 -0
- data/lib/assembly/single_ended_assembler.rb +441 -0
- data/lib/assembly/velvet_c_binding.rb +54 -0
- data/lib/assembly/velvet_graph_sequence_extractor.rb +123 -0
- data/lib/external/VERSION +1 -0
- data/lib/finishm/assemble.rb +224 -0
- data/lib/finishm/explore.rb +217 -0
- data/lib/finishm/finisher.rb +303 -0
- data/lib/finishm/fluff.rb +122 -0
- data/lib/finishm/gapfiller.rb +325 -0
- data/lib/finishm/orfs_finder.rb +88 -0
- data/lib/finishm/path_counter.rb +90 -0
- data/lib/finishm/primers.rb +425 -0
- data/lib/finishm/primers_check.rb +176 -0
- data/lib/finishm/roundup.rb +344 -0
- data/lib/finishm/sequence.rb +142 -0
- data/lib/finishm/visualise.rb +430 -0
- data/lib/finishm/wander.rb +270 -0
- data/lib/kmer_abundance_pattern.rb +79 -0
- data/lib/kmer_multi_abundance_file.rb +48 -0
- data/lib/oligo_designer.rb +88 -0
- data/lib/priner.rb +66 -0
- data/spec/acyclic_connection_finder_spec.rb +551 -0
- data/spec/all_orfs_spec.rb +443 -0
- data/spec/assemble_spec.rb +186 -0
- data/spec/bubbly_assembler_spec.rb +707 -0
- data/spec/c_node_finder_spec.rb +58 -0
- data/spec/connection_interpreter_spec.rb +284 -0
- data/spec/contig_printer_spec.rb +291 -0
- data/spec/coverage_based_graph_filter_spec.rb +102 -0
- data/spec/data/6_3e4e5e6e.1vANME.bam +0 -0
- data/spec/data/6_3e4e5e6e.1vANME.bam.bai +0 -0
- data/spec/data/acyclic_connection_finder/1/probes.fa +5 -0
- data/spec/data/acyclic_connection_finder/1/random1.fa +2 -0
- data/spec/data/acyclic_connection_finder/1/random1.sammy.fa.gz +0 -0
- data/spec/data/acyclic_connection_finder/1/random2.fa +2 -0
- data/spec/data/acyclic_connection_finder/1/random2.sammy.fa.gz +0 -0
- data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.fa +39 -0
- data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.slightly_changed.fa +39 -0
- data/spec/data/assembly/1_simple_bubble_uneven_coverage/reads_combined.fa.gz +0 -0
- data/spec/data/assembly_visualiser/Contig_6_1_to_250.fa.kmers31 +220 -0
- data/spec/data/assembly_visualiser/Contig_7_1_to_250.fa.kmers31 +220 -0
- data/spec/data/assembly_visualiser/Graph +46 -0
- data/spec/data/assembly_visualiser/start_kmers1 +2 -0
- data/spec/data/bands.csv +1 -0
- data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq +0 -0
- data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq.names +544 -0
- data/spec/data/c_probe_node_finder/1/Graph2 +668 -0
- data/spec/data/c_probe_node_finder/1/LastGraph +668 -0
- data/spec/data/c_probe_node_finder/1/Log +756 -0
- data/spec/data/c_probe_node_finder/1/PreGraph +11 -0
- data/spec/data/c_probe_node_finder/1/Roadmaps +2009 -0
- data/spec/data/c_probe_node_finder/1/contigs.fa +29 -0
- data/spec/data/c_probe_node_finder/1/stats.txt +6 -0
- data/spec/data/contig_printer/1/HOWTO_RECREATE +17 -0
- data/spec/data/contig_printer/1/contigs.fa +4 -0
- data/spec/data/contig_printer/1/seq.fa +2408 -0
- data/spec/data/contig_printer/1/seq.fa.svg +153 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/Graph2 +2953 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/LastGraph +2953 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/Log +21 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/PreGraph +27 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/Roadmaps +5182 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/Sequences +3612 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/contigs.fa +36 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/stats.txt +14 -0
- data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam +0 -0
- data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam.bai +0 -0
- data/spec/data/contig_printer/1/seq.node12.fa +4 -0
- data/spec/data/contig_printer/1/seq1_1to550.fa +2 -0
- data/spec/data/contig_printer/1/seq2_1to550.fa +2 -0
- data/spec/data/contig_printer/1/seq2_1to550.fa.fai +1 -0
- data/spec/data/explore/1/2seqs.sammy.fa +12004 -0
- data/spec/data/explore/1/HOWTO_RECREATE.txt +6 -0
- data/spec/data/explore/1/a.fa +2 -0
- data/spec/data/explore/1/seq1_and_a.fa +3 -0
- data/spec/data/explore/1/seq2.fa +2 -0
- data/spec/data/fluff/1/2seqs.sammy.fa +12004 -0
- data/spec/data/fluff/1/HOWTO_RECREATE.txt +5 -0
- data/spec/data/fluff/1/seq1.fa +2 -0
- data/spec/data/fluff/1/seq2.fa +2 -0
- data/spec/data/gapfilling/1/reads.fa +171 -0
- data/spec/data/gapfilling/1/trail_with_Ns.fa +5 -0
- data/spec/data/gapfilling/1/velvetAssembly/Graph2 +130 -0
- data/spec/data/gapfilling/1/velvetAssembly/LastGraph +130 -0
- data/spec/data/gapfilling/1/velvetAssembly/Log +199 -0
- data/spec/data/gapfilling/1/velvetAssembly/PreGraph +7 -0
- data/spec/data/gapfilling/1/velvetAssembly/Roadmaps +239 -0
- data/spec/data/gapfilling/1/velvetAssembly/Sequences +281 -0
- data/spec/data/gapfilling/1/velvetAssembly/contigs.fa +12 -0
- data/spec/data/gapfilling/1/velvetAssembly/stats.txt +4 -0
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- data/spec/data/gapfilling/2/sammy_reads.fa.gz +0 -0
- data/spec/data/gapfilling/2/with_gaps.fa +4 -0
- data/spec/data/gapfilling/3/HOWTO_recreate +4 -0
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- data/spec/data/gapfilling/4/HOWTO_recreate +1 -0
- data/spec/data/gapfilling/4/reads.fa.gz +0 -0
- data/spec/data/gapfilling/5/HOWTO_RECREATE +7 -0
- data/spec/data/gapfilling/5/answer.fna +2 -0
- data/spec/data/gapfilling/5/gappy.fna +2 -0
- data/spec/data/gapfilling/5/reads.fa +17961 -0
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- data/spec/data/gapfilling/6/random1.fa +28 -0
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- data/spec/data/gapfilling/6/to_gapfill.fa +22 -0
- data/spec/data/kmer_profile_to_assembly/multiple_abundance_file1.csv +2 -0
- data/spec/data/kmers_count1.csv +2 -0
- data/spec/data/kmers_count2.csv +3 -0
- data/spec/data/out +3 -0
- data/spec/data/positive_latching_pair.fa +2 -0
- data/spec/data/primers.csv +4 -0
- data/spec/data/read_selection_by_kmer/blacklist1.txt +1 -0
- data/spec/data/read_selection_by_kmer/input.fasta +6 -0
- data/spec/data/read_selection_by_kmer/whitelist1.txt +1 -0
- data/spec/data/read_selection_by_kmer/whitelist2.txt +2 -0
- data/spec/data/read_to_node/1_a_graph/HOWTO_RECREATE.txt +2 -0
- data/spec/data/read_to_node/1_a_graph/LastGraph +6695 -0
- data/spec/data/read_to_node/1_a_graph/ReadToNode.bin +0 -0
- data/spec/data/read_to_node/2_no_read256_or_259/HOWTO_RECREATE.txt +3 -0
- data/spec/data/read_to_node/2_no_read256_or_259/LastGraph +6693 -0
- data/spec/data/read_to_node/2_no_read256_or_259/ReadToNode.bin +0 -0
- data/spec/data/read_to_node/3_no_last_read/LastGraph +6694 -0
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- data/spec/data/t/details.txt +5 -0
- data/spec/data/t/details.txt.srt +5 -0
- data/spec/data/t/location.txt +3 -0
- data/spec/data/t/location.txt.srt +3 -0
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- data/spec/data/tweak/1_gap_then_unscaffolded/scaffolds.fa +6 -0
- data/spec/data/tweak/2_second_genome/answer2.fa +2 -0
- data/spec/data/tweak/2_second_genome/reads.fa.gz +0 -0
- data/spec/data/tweak/3_variant/answer.fa +2 -0
- data/spec/data/tweak/3_variant/lesser_answer.fa +2 -0
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- data/spec/data/velvet_test_trails/Assem/Log +35 -0
- data/spec/data/velvet_test_trails/Assem/PreGraph +9 -0
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- data/spec/data/velvet_test_trails/read1.fa +2 -0
- data/spec/data/velvet_test_trails/reads.fa +50 -0
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- data/spec/data/wander/1/random1.fa +2 -0
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- data/spec/depth_first_search_spec.rb +190 -0
- data/spec/dijkstra_spec.rb +143 -0
- data/spec/explore_spec.rb +29 -0
- data/spec/fluffer_spec.rb +155 -0
- data/spec/gapfiller_spec.rb +107 -0
- data/spec/graph_explorer_spec.rb +475 -0
- data/spec/graph_generator_spec.rb +99 -0
- data/spec/height_finder_spec.rb +306 -0
- data/spec/kmer_abundance_pattern_spec.rb +56 -0
- data/spec/kmer_coverage_based_path_filter_spec.rb +73 -0
- data/spec/kmer_profile_finder_spec.rb +38 -0
- data/spec/kmers_count_tabulate_spec.rb +120 -0
- data/spec/oriented_node_trail_spec.rb +221 -0
- data/spec/paired_end_neighbours_spec.rb +126 -0
- data/spec/paths_between_nodes_spec.rb +349 -0
- data/spec/priner_spec.rb +7 -0
- data/spec/read_input_spec.rb +23 -0
- data/spec/read_selection_by_kmer_spec.rb +166 -0
- data/spec/read_to_node_spec.rb +35 -0
- data/spec/roundup_spec.rb +366 -0
- data/spec/scaffold_breaker_spec.rb +144 -0
- data/spec/sequence_spec.rb +43 -0
- data/spec/single_coherent_paths_between_nodes_spec.rb +492 -0
- data/spec/single_coherent_wanderer_spec.rb +120 -0
- data/spec/single_ended_assembler_spec.rb +398 -0
- data/spec/spec_helper.rb +310 -0
- data/spec/velvet_graph_sequence_extractor_spec.rb +80 -0
- data/spec/visualise_spec.rb +105 -0
- data/spec/wander_spec.rb +119 -0
- data/spec/watch_for_changes.sh +16 -0
- data/validation/fasta_compare.rb +72 -0
- data/validation/gapfill_simulate_perfect.rb +108 -0
- metadata +899 -0
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require 'set'
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module Bio::AssemblyGraphAlgorithms
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class CoverageBasedGraphFilter
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include Bio::FinishM::Logging
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# Remove all nodes from the graph that do not have sufficient coverage
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# (i.e. possibly are sequencing error artefacts)
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#
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# Options:
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# :whitelisted_sequences: provide an enumerable of sequence IDs, don't remove any nodes that have reads tracked to any of these IDs
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#
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# Returns nodes_removed, arcs_removed (as objects, in particular order)
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def remove_low_coverage_nodes(graph, threshold, options = {})
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graph.delete_nodes_if do |node|
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deleting = false
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if node.coverage and (node.coverage < threshold)
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deleting = true
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end
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if deleting and options[:whitelisted_sequences] and !node.short_reads.nil?
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options[:whitelisted_sequences].each do |seq_id|
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if node.short_reads.collect{|r| r.read_id}.include?(seq_id)
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deleting = false
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log.debug "Preserving low coverage but whitelisted node: #{node.node_id}" if log.debug?
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end
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end
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end
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deleting
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end
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end
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end
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class ConnectivityBasedGraphFilter
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include Bio::FinishM::Logging
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# Remove parts of the graph that are unconnected to any whitelisted nodes
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#
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# options:
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# :leash_length: don't explore more than this length away from each of the whitelisted_nodes. Defualt nil, no bounds
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def remove_unconnected_nodes(graph, whitelisted_nodes, options={})
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# Copy the whitelist
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all_whitelisted_nodes = Set.new whitelisted_nodes
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dij = Bio::AssemblyGraphAlgorithms::Dijkstra.new
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dij_options = {:ignore_directions => true}
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dij_options[:leash_length] = options[:leash_length]
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# Depth-first search of all the connected parts looking for nodes to keep
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whitelisted_nodes.each do |originally_whitelisted_node|
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onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new
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onode.node = originally_whitelisted_node
|
53
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+
onode.first_side = Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST #irrelevant which is first because :ignore_directions => true
|
54
|
+
log.debug "Testing for connectivity from #{onode.node.node_id}" if log.debug?
|
55
|
+
|
56
|
+
min_distances = dij.min_distances(graph, onode, dij_options)
|
57
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+
min_distances.each do |key, distance|
|
58
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+
all_whitelisted_nodes << graph.nodes[key[0]]
|
59
|
+
end
|
60
|
+
end
|
61
|
+
|
62
|
+
# Delete all nodes that aren't in the
|
63
|
+
graph.delete_nodes_if do |node|
|
64
|
+
!all_whitelisted_nodes.include?(node)
|
65
|
+
end
|
66
|
+
end
|
67
|
+
end
|
68
|
+
end
|
@@ -0,0 +1,63 @@
|
|
1
|
+
require 'ds'
|
2
|
+
require 'set'
|
3
|
+
|
4
|
+
module Bio
|
5
|
+
module Velvet
|
6
|
+
class Graph
|
7
|
+
# Do a depth first search starting at this oriented node,
|
8
|
+
# yielding an OrientedNodeTrail at each new node encountered.
|
9
|
+
# The new node is the last node in the yielded trail. The result
|
10
|
+
# of the yield tells whether this method whether to abandon
|
11
|
+
# searching further from this point (false)
|
12
|
+
# or keep going (true).
|
13
|
+
def depth_first_search(oriented_node)
|
14
|
+
log = Bio::Log::LoggerPlus['finishm']
|
15
|
+
discovered_oriented_nodes = Set.new
|
16
|
+
|
17
|
+
# Traverse through the graph, yielding at each new node
|
18
|
+
current_path = Bio::Velvet::Graph::OrientedNodeTrail.new
|
19
|
+
current_path.add_oriented_node oriented_node
|
20
|
+
|
21
|
+
stack = DS::Stack.new
|
22
|
+
stack.push current_path
|
23
|
+
|
24
|
+
# While there is more on the stack
|
25
|
+
while current_path = stack.pop
|
26
|
+
log.debug "Perhaps #{current_path.last}?" if log.debug?
|
27
|
+
if discovered_oriented_nodes.include?(path_to_searchable(current_path))
|
28
|
+
# Already seen this node, do nothing with it
|
29
|
+
log.debug "Skipping #{current_path.last} since that has already been seen" if log.debug?
|
30
|
+
next
|
31
|
+
else
|
32
|
+
log.debug "That's a new node, #{current_path.last}" if log.debug?
|
33
|
+
# Found a new node for the user to play with
|
34
|
+
discovered_oriented_nodes << path_to_searchable(current_path)
|
35
|
+
|
36
|
+
continue = yield current_path
|
37
|
+
|
38
|
+
# prep for next time if required.
|
39
|
+
if continue
|
40
|
+
# Sort node IDs to simplify testing
|
41
|
+
next_nodes = current_path.neighbours_of_last_node(self).sort{|n1, n2|
|
42
|
+
-(n1.node.node_id <=> n2.node.node_id)
|
43
|
+
}
|
44
|
+
next_nodes.each do |n|
|
45
|
+
path = current_path.copy
|
46
|
+
path.add_oriented_node n
|
47
|
+
stack.push path
|
48
|
+
end
|
49
|
+
end
|
50
|
+
end
|
51
|
+
end
|
52
|
+
end
|
53
|
+
|
54
|
+
private
|
55
|
+
# Set#include? doesn't pick up when the same OrientedNode is picked
|
56
|
+
# up twice independently, I don't think. So convert to an array first
|
57
|
+
def path_to_searchable(path)
|
58
|
+
last = path.last
|
59
|
+
return [last.node.node_id, last.first_side]
|
60
|
+
end
|
61
|
+
end
|
62
|
+
end
|
63
|
+
end
|
@@ -0,0 +1,216 @@
|
|
1
|
+
require 'ds'
|
2
|
+
require 'set'
|
3
|
+
|
4
|
+
class Bio::AssemblyGraphAlgorithms::Dijkstra
|
5
|
+
include Bio::FinishM::Logging
|
6
|
+
|
7
|
+
# Return an array of DistancedOrientedNode objects, those reachable from
|
8
|
+
# the initial_oriented_node. options:
|
9
|
+
# :leash_length => max distance explored,
|
10
|
+
# can be set to nil to search indefinitely
|
11
|
+
# :ignore_directions: => true or false (default). If true, explore direction-independently.
|
12
|
+
# i.e. if 1s->3s and 2s->3s, then include 2s in the returned set of min_distances
|
13
|
+
# and continue exploring from 2s. Return each found node twice, once for each direction
|
14
|
+
# :neighbour_finder => an object that responds to #neighbours(oriented_node) and
|
15
|
+
# returns an array of Bio::FinishM::PairedEndNeighbourFinder::Neighbour objects
|
16
|
+
# default: just search using OrientedNode#next_neighbours
|
17
|
+
# :max_nodes => maximum number of nodes to return, to prevent out of control
|
18
|
+
# exploring of the graph. If there is plenty of nodes to explore, then the
|
19
|
+
# length of the returned hash is options[:max_nodes]+1 (+1 because the starting
|
20
|
+
# node is included). It will probably be longer if :ignore_directions == true, in that
|
21
|
+
# case the number of node_ids is constrained. It may also be longer if there is ties
|
22
|
+
# at the edges of the constrained exploration.
|
23
|
+
#
|
24
|
+
# Returns a Hash of [node_id, first_side] => distance
|
25
|
+
def min_distances(graph, initial_oriented_node, options={})
|
26
|
+
pqueue = DS::AnyPriorityQueue.new {|a,b| a < b}
|
27
|
+
first = DistancedOrientedNode.new
|
28
|
+
first.node = initial_oriented_node.node
|
29
|
+
first.first_side = initial_oriented_node.first_side
|
30
|
+
first.distance = 0
|
31
|
+
pqueue.push first, first.distance
|
32
|
+
|
33
|
+
to_return = {}
|
34
|
+
first_node = true
|
35
|
+
found_nodes = Set.new([first.node.node_id])
|
36
|
+
|
37
|
+
while min_distanced_node = pqueue.shift
|
38
|
+
|
39
|
+
# Add/overwrite the current one
|
40
|
+
to_return[min_distanced_node.to_settable] = min_distanced_node.distance
|
41
|
+
|
42
|
+
log.debug "Working from #{min_distanced_node.inspect}" if log.debug?
|
43
|
+
|
44
|
+
if options[:leash_length] and min_distanced_node.distance > options[:leash_length]
|
45
|
+
# we are passed leash length, and this is the nearest node. So we are finito.
|
46
|
+
log.debug "passed the leash length, cutting short our travels" if log.debug?
|
47
|
+
break
|
48
|
+
end
|
49
|
+
|
50
|
+
if options[:max_nodes] and found_nodes.length > options[:max_nodes]
|
51
|
+
log.debug "passed max-nodes threshold and have #{found_nodes.length} nodes" if log.debug?
|
52
|
+
# remove extras that may have been queued if we are over the limit
|
53
|
+
distances_direction_agnostic = {}
|
54
|
+
to_return.each do |key, distance|
|
55
|
+
prev = distances_direction_agnostic[key[0]]
|
56
|
+
if prev.nil? or prev > distance
|
57
|
+
distances_direction_agnostic[key[0]] = distance
|
58
|
+
end
|
59
|
+
end
|
60
|
+
if distances_direction_agnostic.length > options[:max_nodes]
|
61
|
+
sorted = distances_direction_agnostic.to_a.sort{|a,b| a[1]<=>b[1]}
|
62
|
+
# deal with ties i.e. at the edge there can be multiple neighbours
|
63
|
+
last_distance = sorted[options[:max_nodes]][1]
|
64
|
+
|
65
|
+
# only keep those nodes that are sufficiently close
|
66
|
+
to_return.select! do |key, distance|
|
67
|
+
distance <= last_distance
|
68
|
+
end
|
69
|
+
end
|
70
|
+
break
|
71
|
+
end
|
72
|
+
|
73
|
+
# Queue nodes after this one
|
74
|
+
current_distance = min_distanced_node.distance
|
75
|
+
|
76
|
+
# Find neighbouring nodes
|
77
|
+
neighbours = nil
|
78
|
+
if options[:neighbour_finder]
|
79
|
+
neighbours = options[:neighbour_finder].neighbours(min_distanced_node)
|
80
|
+
else
|
81
|
+
neighbours = min_distanced_node.next_neighbours(graph)
|
82
|
+
end
|
83
|
+
|
84
|
+
# explore each neighbour node
|
85
|
+
neighbours.each do |onode|
|
86
|
+
found_nodes << onode.node.node_id
|
87
|
+
new_distance = current_distance
|
88
|
+
if options[:neighbour_finder]
|
89
|
+
# Don't use negative distances as this algorithm cannot handle it, and it is impossible
|
90
|
+
# anyway
|
91
|
+
if onode.distance > 0
|
92
|
+
new_distance += onode.distance
|
93
|
+
else
|
94
|
+
new_distance += 0
|
95
|
+
end
|
96
|
+
end
|
97
|
+
unless first_node
|
98
|
+
new_distance += min_distanced_node.node.length_alone
|
99
|
+
end
|
100
|
+
|
101
|
+
if to_return[onode.to_settable] and to_return[onode.to_settable] <= new_distance
|
102
|
+
# We already know a shorter path to this neighbour, so ignore it
|
103
|
+
log.debug "Already seen this node at the same or shorter distance, going no further" if log.debug?
|
104
|
+
else
|
105
|
+
log.debug "Queuing new distance for neighbour: #{onode}: #{new_distance}" if log.debug?
|
106
|
+
# new shortest distance found. queue it up
|
107
|
+
distanced_node = DistancedOrientedNode.new
|
108
|
+
distanced_node.node = onode.node
|
109
|
+
distanced_node.first_side = onode.first_side
|
110
|
+
distanced_node.distance = new_distance
|
111
|
+
to_return[onode.to_settable] = new_distance
|
112
|
+
pqueue.push distanced_node, new_distance
|
113
|
+
|
114
|
+
if options[:ignore_directions]
|
115
|
+
reverse = DistancedOrientedNode.new
|
116
|
+
reverse.node = onode.node
|
117
|
+
reverse.first_side = onode.reverse.first_side
|
118
|
+
reverse.distance = new_distance
|
119
|
+
to_return[onode.to_settable] = new_distance
|
120
|
+
pqueue.push reverse, new_distance
|
121
|
+
end
|
122
|
+
end
|
123
|
+
end
|
124
|
+
|
125
|
+
first_node = false
|
126
|
+
end
|
127
|
+
|
128
|
+
# if ignore directions, then fixup the return so that each direction is included
|
129
|
+
if options[:ignore_directions]
|
130
|
+
new_to_return = {}
|
131
|
+
to_return.each do |key, distance|
|
132
|
+
keys = [
|
133
|
+
Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST,
|
134
|
+
Bio::Velvet::Graph::OrientedNodeTrail::END_IS_FIRST].collect do |direction|
|
135
|
+
[key[0], direction]
|
136
|
+
end
|
137
|
+
new_distance = keys.collect{|k| to_return[k]}.reject{|d| d.nil?}.min
|
138
|
+
keys.each do |key|
|
139
|
+
new_to_return[key] = new_distance
|
140
|
+
end
|
141
|
+
end
|
142
|
+
to_return = new_to_return
|
143
|
+
end
|
144
|
+
|
145
|
+
return to_return
|
146
|
+
end
|
147
|
+
|
148
|
+
# like #min_distances except explores in both directions
|
149
|
+
def min_distances_in_both_directions(graph, node, options={})
|
150
|
+
all_min_distances = {}
|
151
|
+
[
|
152
|
+
Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST,
|
153
|
+
Bio::Velvet::Graph::OrientedNodeTrail::END_IS_FIRST,
|
154
|
+
].each do |direction|
|
155
|
+
onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new(node, direction)
|
156
|
+
min_distances = min_distances(graph, onode, options)
|
157
|
+
min_distances.each do |node_direction, distance|
|
158
|
+
current = all_min_distances[node_direction]
|
159
|
+
unless current and current > distance
|
160
|
+
all_min_distances[node_direction] = distance
|
161
|
+
end
|
162
|
+
end
|
163
|
+
end
|
164
|
+
return all_min_distances
|
165
|
+
end
|
166
|
+
|
167
|
+
def min_distances_from_many_nodes_in_both_directions(graph, nodes, options={})
|
168
|
+
all_min_distances = {}
|
169
|
+
nodes.each do |node|
|
170
|
+
[
|
171
|
+
Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST,
|
172
|
+
Bio::Velvet::Graph::OrientedNodeTrail::END_IS_FIRST,
|
173
|
+
].each do |direction|
|
174
|
+
onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new(node, direction)
|
175
|
+
min_distances = min_distances(graph, onode, options)
|
176
|
+
min_distances.each do |node_direction, distance|
|
177
|
+
current = all_min_distances[node_direction]
|
178
|
+
unless current and current > distance
|
179
|
+
all_min_distances[node_direction] = distance
|
180
|
+
end
|
181
|
+
end
|
182
|
+
end
|
183
|
+
end
|
184
|
+
return all_min_distances
|
185
|
+
end
|
186
|
+
|
187
|
+
# An oriented node some distance from the origin of exploration
|
188
|
+
class DistancedOrientedNode
|
189
|
+
attr_accessor :node, :first_side, :distance
|
190
|
+
|
191
|
+
# Using Set object, often we want two separate objects to be considered equal even if
|
192
|
+
# they are distinct objects
|
193
|
+
def to_settable
|
194
|
+
[@node.node_id, @first_side]
|
195
|
+
end
|
196
|
+
|
197
|
+
# Which side of the node is not first?
|
198
|
+
def second_side
|
199
|
+
@first_side == Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST ?
|
200
|
+
Bio::Velvet::Graph::OrientedNodeTrail::END_IS_FIRST :
|
201
|
+
Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST
|
202
|
+
end
|
203
|
+
|
204
|
+
def next_neighbours(graph)
|
205
|
+
onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new
|
206
|
+
onode.node = @node
|
207
|
+
onode.first_side = @first_side
|
208
|
+
return onode.next_neighbours(graph)
|
209
|
+
end
|
210
|
+
|
211
|
+
def inspect
|
212
|
+
"DistancedOrientedNode #{object_id}: node=#{@node.node_id} first=#{@first_side} distance=#{@distance}"
|
213
|
+
end
|
214
|
+
alias_method :to_s, :inspect
|
215
|
+
end
|
216
|
+
end
|
@@ -0,0 +1,253 @@
|
|
1
|
+
require 'ds'
|
2
|
+
require 'set'
|
3
|
+
|
4
|
+
module Bio
|
5
|
+
module AssemblyGraphAlgorithms
|
6
|
+
class Fluffer
|
7
|
+
include Bio::FinishM::Logging
|
8
|
+
BEYOND_LEASH_LENGTH_FATE = :beyond_leash_length
|
9
|
+
TERMINAL_NODE_FATE = :terminal_node
|
10
|
+
DEAD_END_FATE = :dead_end
|
11
|
+
|
12
|
+
|
13
|
+
class FlufferHalfResult
|
14
|
+
attr_accessor :golden_paths, :golden_path_fragments, :golden_path_fates
|
15
|
+
|
16
|
+
def initialize
|
17
|
+
@golden_paths = []
|
18
|
+
@golden_path_fragments = []
|
19
|
+
end
|
20
|
+
end
|
21
|
+
|
22
|
+
# Holds an array of paths, but also the fates of each of those paths - why were they halted?
|
23
|
+
class FlufferPathSet < Array
|
24
|
+
attr_accessor :fates
|
25
|
+
|
26
|
+
def initialize
|
27
|
+
@fates = []
|
28
|
+
end
|
29
|
+
end
|
30
|
+
|
31
|
+
# Return an array of array of paths.
|
32
|
+
def fluff(finishm_graph, leash_length, options={})
|
33
|
+
log.debug "Fluffing part 1.." if log.debug?
|
34
|
+
half_results = fluff_part1(finishm_graph, leash_length, options)
|
35
|
+
|
36
|
+
log.debug "Found fluff half results: #{half_results}" if log.debug?
|
37
|
+
log.debug "Fluffing part 2.." if log.debug?
|
38
|
+
return fluff_part2(half_results)
|
39
|
+
end
|
40
|
+
|
41
|
+
def fluff_part1(finishm_graph, leash_length, options={})
|
42
|
+
# Get a set of all probes so that they can be checked against
|
43
|
+
log.debug "Found #{finishm_graph.probe_nodes.reject{|node| node.nil?}.length} different probes that were in the final velvet graph" if log.debug?
|
44
|
+
half_results = []
|
45
|
+
graph = finishm_graph.graph
|
46
|
+
|
47
|
+
# For each probe in the graph
|
48
|
+
finishm_graph.probe_nodes.each_with_index do |node, probe_index|
|
49
|
+
|
50
|
+
# If the node is not found in the graph, then forget it
|
51
|
+
if node.nil?
|
52
|
+
half_results.push FlufferHalfResult.new
|
53
|
+
|
54
|
+
else # probe was found in the graph. Start finding them paths.
|
55
|
+
# start exploring the squid way
|
56
|
+
golden_paths = [] #These is the full paths found
|
57
|
+
golden_fragments = [] #paths to join up to the end
|
58
|
+
already_visited_nodes = Set.new #Nodes that have already been explored
|
59
|
+
golden_path_fates = [] #An array of how each of the paths were halted
|
60
|
+
|
61
|
+
golden_onodes = Set.new #Nodes that stop exploration
|
62
|
+
terminal_nodes = Set.new
|
63
|
+
# Add all the nodes that are being probed, because we don't want double exploration
|
64
|
+
# i.e. want probe1 => probe2, probe2 => probe3, but not probe1 => probe2 => probe3
|
65
|
+
finishm_graph.probe_nodes.each_with_index do |node, probe_index2|
|
66
|
+
# Don't add the node itself. This is a special case which is already handled below
|
67
|
+
unless probe_index == probe_index2 or node.nil?
|
68
|
+
terminal_nodes << finishm_graph.velvet_oriented_node(probe_index2).to_settable
|
69
|
+
end
|
70
|
+
end
|
71
|
+
|
72
|
+
stack = DS::Stack.new
|
73
|
+
stack.push finishm_graph.initial_path_from_probe(probe_index)
|
74
|
+
|
75
|
+
while current_path = stack.pop
|
76
|
+
log.debug "Perhaps #{current_path}?" if log.debug?
|
77
|
+
if golden_onodes.include?(current_path.last.to_settable)
|
78
|
+
# Probably a golden fragment, unless the node found is in the current path.
|
79
|
+
# if that is true, that's a loop along a golden path.
|
80
|
+
first_index = nil
|
81
|
+
current_path.each_with_index do |directed_node, i|
|
82
|
+
if directed_node.node == current_path.last.node and
|
83
|
+
directed_node.first_side == current_path.last.first_side
|
84
|
+
first_index = i
|
85
|
+
break
|
86
|
+
end
|
87
|
+
end
|
88
|
+
|
89
|
+
if first_index == current_path.length-1
|
90
|
+
# Found another golden path(s)
|
91
|
+
log.debug "Ran into a golden node" if log.debug?
|
92
|
+
golden_fragments.push current_path
|
93
|
+
current_path.each do |onode|
|
94
|
+
golden_onodes << onode.to_settable
|
95
|
+
end
|
96
|
+
else
|
97
|
+
# Loop found along a golden path or fragment
|
98
|
+
log.debug "Found a loop along a golden path: #{current_path}" if log.debug?
|
99
|
+
next
|
100
|
+
end
|
101
|
+
elsif already_visited_nodes.include?(current_path.last.to_settable) and
|
102
|
+
!terminal_nodes.include?(current_path.last.to_settable)
|
103
|
+
# Already seen this (non-golden) node, do nothing with it
|
104
|
+
log.debug "Skipping #{current_path.last} since that has already been seen" if log.debug?
|
105
|
+
next
|
106
|
+
else
|
107
|
+
if log.debug?
|
108
|
+
second_last_node = current_path[current_path.length-2]
|
109
|
+
second_last_node ||= 'initial_node'
|
110
|
+
log.debug "That's a new node, #{second_last_node}/#{current_path.last}" if log.debug?
|
111
|
+
end
|
112
|
+
|
113
|
+
# if we aren't beyond the leash. Presumably this
|
114
|
+
# doesn't happen much, but there is a possibility that the leash will
|
115
|
+
# prevent a real path being discovered. If there is two or more paths to a node
|
116
|
+
# and a path longer than the leash is discovered first, then all the
|
117
|
+
# nodes on that leash will be marked as discovered when they really aren't
|
118
|
+
# TODO: fix the above bug
|
119
|
+
if leash_length.nil? or current_path.length_in_bp < leash_length
|
120
|
+
# Found a new node for the user to play with
|
121
|
+
already_visited_nodes << current_path.last.to_settable
|
122
|
+
|
123
|
+
# Have we found a path to one of the other probes?
|
124
|
+
if terminal_nodes.include?(current_path.last.to_settable)
|
125
|
+
log.debug "Found the terminal node: #{current_path}" if log.debug?
|
126
|
+
golden_paths.push current_path
|
127
|
+
golden_path_fates.push TERMINAL_NODE_FATE
|
128
|
+
|
129
|
+
else # Use an else statement here because we want exploration to stop when other probes are encountered
|
130
|
+
|
131
|
+
# prep for next time
|
132
|
+
# Sort node IDs to simplify testing
|
133
|
+
next_nodes = current_path.neighbours_of_last_node(graph).sort{|n1, n2|
|
134
|
+
-(n1.node.node_id <=> n2.node.node_id)
|
135
|
+
}
|
136
|
+
next_nodes.each do |n|
|
137
|
+
path = current_path.copy
|
138
|
+
path.add_oriented_node n
|
139
|
+
log.debug "Pushing a path yet to be explored: #{path}" if log.debug?
|
140
|
+
stack.push path
|
141
|
+
end
|
142
|
+
|
143
|
+
# If we are at a dead end, add this whole path as a golden path. This
|
144
|
+
# is low coverage fluff, perhaps. Or it is nothing.
|
145
|
+
if next_nodes.empty?
|
146
|
+
log.debug "Found a dead end path: #{current_path}" if log.debug?
|
147
|
+
golden_paths.push current_path
|
148
|
+
golden_path_fates.push DEAD_END_FATE
|
149
|
+
current_path.each do |onode|
|
150
|
+
golden_onodes << onode.to_settable
|
151
|
+
end
|
152
|
+
end
|
153
|
+
end
|
154
|
+
else
|
155
|
+
if log.debug?
|
156
|
+
log.debug "Found a path that made it to the end of the leash, with path length #{current_path.length_in_bp} vs leash length #{leash_length}"
|
157
|
+
log.debug "Path given up on: #{current_path}"
|
158
|
+
log.debug "Path sequence given up on: #{current_path.sequence}"
|
159
|
+
log.debug "Node lengths: #{current_path.collect{|n| n.node.length_alone}.join(',')}"
|
160
|
+
end
|
161
|
+
# Record this past-leash-length path
|
162
|
+
golden_paths.push current_path
|
163
|
+
golden_path_fates.push BEYOND_LEASH_LENGTH_FATE
|
164
|
+
current_path.each do |onode|
|
165
|
+
golden_onodes << onode.to_settable
|
166
|
+
end
|
167
|
+
end
|
168
|
+
end
|
169
|
+
end
|
170
|
+
|
171
|
+
log.debug "Found #{golden_paths.length} golden paths and #{golden_fragments.length} golden fragments" if log.debug?
|
172
|
+
fluff_half_result = FlufferHalfResult.new
|
173
|
+
fluff_half_result.golden_paths = golden_paths
|
174
|
+
fluff_half_result.golden_path_fragments = golden_fragments
|
175
|
+
fluff_half_result.golden_path_fates = golden_path_fates
|
176
|
+
|
177
|
+
half_results.push fluff_half_result
|
178
|
+
end
|
179
|
+
end
|
180
|
+
|
181
|
+
return half_results
|
182
|
+
end
|
183
|
+
|
184
|
+
def fluff_part2(half_results)
|
185
|
+
all_all_paths = []
|
186
|
+
|
187
|
+
half_results.each do |segment_half_result|
|
188
|
+
# OK, so we've transformed the data into a state where there is
|
189
|
+
# at least one path through the data
|
190
|
+
# and tentacles hanging off various golden nodes.
|
191
|
+
# Now separate out the paths and return the array.
|
192
|
+
# First transform the data so it can be referenced by the end node
|
193
|
+
terminal_golden_nodes_to_paths = {}
|
194
|
+
segment_half_result.golden_path_fragments.each do |fragment|
|
195
|
+
l = fragment.last.to_settable
|
196
|
+
terminal_golden_nodes_to_paths[l] ||= []
|
197
|
+
terminal_golden_nodes_to_paths[l].push fragment
|
198
|
+
end
|
199
|
+
# Next backtrack through the paths
|
200
|
+
# Each path starts at the beginning and ends at a
|
201
|
+
# golden node
|
202
|
+
all_paths = FlufferPathSet.new
|
203
|
+
stack = DS::Stack.new
|
204
|
+
# Push the golden path and all paths that finish at the last node
|
205
|
+
segment_half_result.golden_paths.each_with_index do |golden_path, i|
|
206
|
+
stack.push [golden_path, 0, segment_half_result.golden_path_fates[i]]
|
207
|
+
end
|
208
|
+
|
209
|
+
while array = stack.pop
|
210
|
+
current_path = array[0]
|
211
|
+
num_to_ignore = array[1]
|
212
|
+
fate = array[2]
|
213
|
+
|
214
|
+
log.debug "Defragging #{current_path.to_s}/#{fate}, ignoring the last #{num_to_ignore} nodes" if log.debug?
|
215
|
+
all_paths.push current_path
|
216
|
+
all_paths.fates.push fate
|
217
|
+
|
218
|
+
# Iterate down this path, spawning new paths if there
|
219
|
+
# are paths that intersect
|
220
|
+
passed_nodes = []
|
221
|
+
current_path.trail.reverse.each_with_index do |onode, i|
|
222
|
+
unless i < num_to_ignore #ignore the last one(s) because they've already been handled
|
223
|
+
frags = terminal_golden_nodes_to_paths[onode.to_settable]
|
224
|
+
log.debug "Offshoots from #{onode}: #{frags.nil? ? '[]' : frags.collect{|f| f.collect{|n| n.node_id}.join(',')}.join(' and ')}" if log.debug?
|
225
|
+
if frags
|
226
|
+
frags.each do |fragment|
|
227
|
+
log.debug "Using an offshoot: #{fragment.to_s}" if log.debug?
|
228
|
+
# The fragment extends from the beginning to the golden node,
|
229
|
+
# the current node. So create a new complete path,
|
230
|
+
# And push it to the stack.
|
231
|
+
new_golden = fragment.copy
|
232
|
+
log.debug "Adding #{new_golden.to_s} and #{passed_nodes.collect{|n| n.node_id}}" if log.debug?
|
233
|
+
passed_nodes.reverse.each_with_index do |onode, i|
|
234
|
+
new_golden.add_oriented_node onode
|
235
|
+
end
|
236
|
+
log.debug "Enqueueing: #{new_golden.to_s} ignoring the last #{i+1} nodes" if log.debug?
|
237
|
+
stack.push [new_golden, i+1, fate]
|
238
|
+
end
|
239
|
+
end
|
240
|
+
end
|
241
|
+
passed_nodes.push onode
|
242
|
+
end
|
243
|
+
end
|
244
|
+
|
245
|
+
# All the paths are in an array, just a linear series of distinct paths
|
246
|
+
all_all_paths.push all_paths
|
247
|
+
end
|
248
|
+
|
249
|
+
return all_all_paths
|
250
|
+
end
|
251
|
+
end
|
252
|
+
end
|
253
|
+
end
|