New upstream version 0.4.8+dfsg (2c389812) · Commits · Debian Med / unicycler

README.md

+2 −0

Original line number	Diff line number	Diff line
		@@ -428,6 +428,8 @@ SPAdes assembly:
		--depth_filter DEPTH_FILTER Filter out contigs lower than this fraction of the chromosomal
		depth, if doing so does not result in graph dead ends (default:
		0.25)
		--largest_component Only keep the largest connected component of the assembly graph
		(default: keep all connected components)
		--spades_tmp_dir SPADES_TMP_DIR
		Specify SPAdes temporary directory using the SPAdes --tmp-dir
		option (default: make a temporary directory in the output

unicycler/assembly_graph.py

+31 −2

Original line number	Diff line number	Diff line
		@@ -423,6 +423,7 @@ class AssemblyGraph(object):
		3) deleting the segment would not create any dead ends
		"""
		segment_nums_to_remove = []
		total_length_removed = 0
		ten_longest_contigs = sorted(self.segments.values(), reverse=True,
		key=lambda x: x.get_length())[:10]
		whole_graph_cutoff = self.get_median_read_depth(ten_longest_contigs) * relative_depth_cutoff
		@@ -437,7 +438,9 @@ class AssemblyGraph(object):
		self.all_segments_below_depth(component, whole_graph_cutoff) or \
		self.dead_end_change_if_deleted(seg_num) <= 0:
		segment_nums_to_remove.append(seg_num)
		total_length_removed += segment.get_length()
		self.remove_segments(segment_nums_to_remove)
		return len(segment_nums_to_remove), total_length_removed

		def filter_homopolymer_loops(self):
		"""
		@@ -455,6 +458,28 @@ class AssemblyGraph(object):
		log.log('Removed homopolymer loops:', 3)
		log.log_number_list(segment_nums_to_remove, 3)

		def choose_largest_component(self):
		"""
		Special logic: throw out all of the graph's connected components except for the largest one.
		"""
		largest_component_length = None
		connected_components = self.get_connected_components()
		for component_nums in connected_components:
		component_segments = [self.segments[x] for x in component_nums]
		component_length = sum(x.get_length() for x in component_segments)
		if largest_component_length is None or component_length > largest_component_length:
		largest_component_length = component_length
		segment_nums_to_remove = []
		for component_nums in connected_components:
		component_segments = [self.segments[x] for x in component_nums]
		component_length = sum(x.get_length() for x in component_segments)
		if component_length < largest_component_length:
		segment_nums_to_remove += component_nums
		self.remove_segments(segment_nums_to_remove)
		if segment_nums_to_remove:
		log.log('\nRemoved not-largest components:', 3)
		log.log_number_list(segment_nums_to_remove, 3)

		def remove_segments(self, nums_to_remove):
		"""
		This function deletes all segments in the nums_to_remove list, along with their links. It
		@@ -923,7 +948,7 @@ class AssemblyGraph(object):
		dead_ends += 1
		return potential_dead_ends - dead_ends

		def clean(self, read_depth_filter):
		def clean(self, read_depth_filter, largest_component):
		"""
		This function does various graph repairs, filters and normalisations to make it a bit
		nicer.
		@@ -931,9 +956,12 @@ class AssemblyGraph(object):
		log.log('Repair multi way junctions ' + get_dim_timestamp(), 3)
		self.repair_multi_way_junctions()
		log.log('Filter by read depth ' + get_dim_timestamp(), 3)
		self.filter_by_read_depth(read_depth_filter)
		removed_count, removed_length = self.filter_by_read_depth(read_depth_filter)
		log.log('Filter homopolymer loops ' + get_dim_timestamp(), 3)
		self.filter_homopolymer_loops()
		if largest_component:
		log.log('Keep largest component ' + get_dim_timestamp(), 3)
		self.choose_largest_component()
		log.log('Merge all possible ' + get_dim_timestamp(), 3)
		self.merge_all_possible(None, 2)
		log.log('Normalise read depths ' + get_dim_timestamp(), 3)
		@@ -943,6 +971,7 @@ class AssemblyGraph(object):
		log.log('Sort link order ' + get_dim_timestamp(), 3)
		self.sort_link_order()
		log.log('Graph cleaning finished ' + get_dim_timestamp(), 3)
		return removed_count, removed_length

		def final_clean(self):
		"""

unicycler/bridge_long_read_simple.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -490,7 +490,7 @@ def get_read_loop_vote(start, end, middle, repeat, strand, minimap_alignments, r
		best_score = test_seq_score
		best_count = loop_count

		# Break when we've hit the max loop count. But if the max isn't our best, then we keep
		# Break when we've hit the max loop count. But if the max is our best, then we keep
		# trying higher.
		if loop_count >= max_tested_loop_count and loop_count != best_count:
		break

unicycler/settings.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -30,8 +30,8 @@ SIMPLE_REPEAT_BRIDGING_BAND_SIZE = 50
		CONTIG_READ_QSCORE = 40

		# This is the maximum number of times an assembly will be Racon polished
		RACON_POLISH_LOOP_COUNT_HYBRID = 5
		RACON_POLISH_LOOP_COUNT_LONG_ONLY = 10
		RACON_POLISH_LOOP_COUNT_HYBRID = 2
		RACON_POLISH_LOOP_COUNT_LONG_ONLY = 4


		# This is the number of times assembly graph contigs are included in the Racon polish reads. E.g.

unicycler/spades_func.py

+10 −4

Original line number	Diff line number	Diff line
		@@ -30,7 +30,8 @@ class BadFastq(Exception):

		def get_best_spades_graph(short1, short2, short_unpaired, out_dir, read_depth_filter, verbosity,
		spades_path, threads, keep, kmer_count, min_k_frac, max_k_frac, kmers,
		no_spades_correct, expected_linear_seqs, spades_tmp_dir):
		no_spades_correct, expected_linear_seqs, spades_tmp_dir,
		largest_component):
		"""
		This function tries a SPAdes assembly at different k-mers and returns the best.
		'The best' is defined as the smallest dead-end count after low-depth filtering. If multiple
		@@ -126,7 +127,7 @@ def get_best_spades_graph(short1, short2, short_unpaired, out_dir, read_depth_fi
		continue

		log.log('\nCleaning k{} graph'.format(kmer), 2)
		assembly_graph.clean(read_depth_filter)
		assembly_graph.clean(read_depth_filter, largest_component)
		clean_graph_filename = os.path.join(spades_dir, ('k%03d' % kmer) + '_assembly_graph.gfa')
		assembly_graph.save_to_gfa(clean_graph_filename, verbosity=2)

		@@ -183,7 +184,7 @@ def get_best_spades_graph(short1, short2, short_unpaired, out_dir, read_depth_fi
		assembly_graph = AssemblyGraph(best_graph_filename, best_kmer, paths_file=paths_file,
		insert_size_mean=insert_size_mean,
		insert_size_deviation=insert_size_deviation)
		assembly_graph.clean(read_depth_filter)
		removed_count, removed_length = assembly_graph.clean(read_depth_filter, largest_component)
		clean_graph_filename = os.path.join(spades_dir, 'k' + str(best_kmer) + '_assembly_graph.gfa')
		assembly_graph.save_to_gfa(clean_graph_filename, verbosity=2)

		@@ -197,9 +198,14 @@ def get_best_spades_graph(short1, short2, short_unpaired, out_dir, read_depth_fi
		row_colour={best_kmer_row: 'green'},
		row_extra_text={best_kmer_row: ' ' + get_left_arrow() + 'best'})

		# Report on the results of the read depth filter (can help with identifying levels of
		# contamination).
		log.log('\nRead depth filter: removed {} contigs totalling {} bp'.format(removed_count,
		removed_length))

		# Clean up.
		if keep < 3 and os.path.isdir(spades_dir):
		log.log('\nDeleting ' + spades_dir + '/')
		log.log('Deleting ' + spades_dir + '/')
		shutil.rmtree(spades_dir, ignore_errors=True)
		if keep < 3 and spades_tmp_dir is not None and os.path.isdir(spades_tmp_dir):
		log.log('Deleting ' + spades_tmp_dir + '/')