README.md

@@ -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

debian/changelog

-unicycler (0.4.7+dfsg-3) UNRELEASED; urgency=medium
+unicycler (0.4.8+dfsg-1) UNRELEASED; urgency=medium
 
-  * Team upload.
+  [ Michael R. Crusoe ]
   * Inherit and use LDFLAGS and CPPFLAGS
   * Mark unicycler-data as Multi-Arch: foreign, as recommended by the
     Multiarch hinter.
-  * Standards-Version: 4.3.0, no changes needed
 
- -- Michael R. Crusoe <michael.crusoe@gmail.com>  Fri, 18 Jan 2019 02:34:45 -0800
+  [ Andreas Tille ]
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Set upstream metadata fields: Repository.
+  * (Build-)Depends: bcftools
+
+ -- Andreas Tille <tille@debian.org>  Tue, 12 Nov 2019 16:01:56 +0100
 
 unicycler (0.4.7+dfsg-2) unstable; urgency=medium
 

debian/compat

-11

debian/control

@@ -4,11 +4,12 @@ Uploaders: Andreas Tille <tille@debian.org>,
            Liubov Chuprikova <chuprikovalv@gmail.com>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
                python3-all,
                python3-setuptools,
                default-jdk,
+               bcftools,
                bowtie2,
                ncbi-blast+,
                pilon,
@@ -17,7 +18,7 @@ Build-Depends: debhelper (>= 11~),
                spades,
                libseqan2-dev,
                zlib1g-dev
-Standards-Version: 4.3.0
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/unicycler
 Vcs-Git: https://salsa.debian.org/med-team/unicycler.git
 Homepage: https://github.com/rrwick/Unicycler
@@ -29,6 +30,7 @@ Depends: ${python3:Depends},
          ${misc:Depends},
          python3-setuptools,
          default-jre,
+         bcftools,
          bowtie2,
          ncbi-blast+,
          pilon,

debian/upstream/metadata

 Reference:
- - Author: >
+- Author: >
     Ryan R. Wick and Louise M. Judd and Claire L. Gorrie and Kathryn
     E. Holt
-   Title: >
+  Title: >
     Unicycler: Resolving bacterial genome assemblies from short and long
     sequencing reads
-   Journal: PLOS Computational Biology
-   Year: 2017
-   Volume: 13
-   Number: 6
-   Pages: e1005595
-   DOI: 10.1371/journal.pcbi.1005595
-   PMID: 28594827
-   URL: "http://journals.plos.org/ploscompbiol/article?id=\
-    10.1371/journal.pcbi.1005595"
-   eprint: "http://journals.plos.org/ploscompbiol/article/\
-    file?id=10.1371/journal.pcbi.1005595&type=printable"
- - Author: >
+  Journal: PLOS Computational Biology
+  Year: 2017
+  Volume: 13
+  Number: 6
+  Pages: e1005595
+  DOI: 10.1371/journal.pcbi.1005595
+  PMID: 28594827
+  URL: "http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005595"
+  eprint: "http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005595&type=printable"
+- Author: >
     Ryan R. Wick and Louise M. Judd and Claire L. Gorrie and Kathryn E. Holt
-   Title: >
+  Title: >
     Completing bacterial genome assemblies with multiplex MinION sequencing
-   Journal: Microbial Genomics
-   Year: 2017
-   Volume: 3
-   Number: 10
-   Pages: e000132
-   DOI: 10.1099/mgen.0.000132
-   PMID: 29177090
-   URL: "http://mgen.microbiologyresearch.org/content/journal/\
-    mgen/10.1099/mgen.0.000132"
-   eprint: "http://mgen.microbiologyresearch.org/deliver/fulltext/\
-    mgen/3/10/mgen000132.pdf?itemId=/content/journal/mgen/10.1099/\
-    mgen.0.000132&mimeType=pdf&isFastTrackArticle="
+  Journal: Microbial Genomics
+  Year: 2017
+  Volume: 3
+  Number: 10
+  Pages: e000132
+  DOI: 10.1099/mgen.0.000132
+  PMID: 29177090
+  URL: "http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000132"
+  eprint: "http://mgen.microbiologyresearch.org/deliver/fulltext/mgen/3/10/mgen000132.pdf?itemId=/content/journal/mgen/10.1099/mgen.0.000132&mimeType=pdf&isFastTrackArticle="
 Registry:
- - Name: OMICtools
-   Entry: OMICS_14591
- - Name: bio.tools
-   Entry: unicycler
- - Name: conda:bioconda
-   Entry: unicycler
- - Name: SciCrunch
-   Entry: NA
+- Name: OMICtools
+  Entry: OMICS_14591
+- Name: bio.tools
+  Entry: unicycler
+- Name: conda:bioconda
+  Entry: unicycler
+- Name: SciCrunch
+  Entry: NA
+Repository: https://github.com/rrwick/Unicycler.git

unicycler/assembly_graph.py

@@ -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

@@ -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

@@ -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

@@ -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 + '/')

unicycler/src/miniasm/hit.cpp

@@ -8,6 +8,7 @@
 #include <limits>
 
 #pragma GCC diagnostic ignored "-Wpragmas"
+#pragma GCC diagnostic ignored "-Wunknown-warning-option"
 #pragma GCC diagnostic ignored "-Wvla"
 #pragma GCC diagnostic ignored "-Wvla-extension"
 #pragma GCC diagnostic ignored "-Wmaybe-uninitialized"

unicycler/unicycler.py

@@ -85,7 +85,7 @@ def main():
                                           args.spades_path, args.threads, args.keep,
                                           args.kmer_count, args.min_kmer_frac, args.max_kmer_frac,
                                           args.kmers, args.no_correct, args.linear_seqs,
-                                          args.spades_tmp_dir)
+                                          args.spades_tmp_dir, args.largest_component)
         determine_copy_depth(graph)
         if args.keep > 0 and not os.path.isfile(best_spades_graph):
             graph.save_to_gfa(best_spades_graph, save_copy_depth_info=True, newline=True,
@@ -346,6 +346,10 @@ def get_arguments():
                               help='Filter out contigs lower than this fraction of the chromosomal '
                                    'depth, if doing so does not result in graph dead ends'
                                    if show_all_args else argparse.SUPPRESS)
+    spades_group.add_argument('--largest_component', action='store_true',
+                              help='Only keep the largest connected component of the assembly '
+                                   'graph (default: keep all connected components)'
+                                   if show_all_args else argparse.SUPPRESS)
     spades_group.add_argument('--spades_tmp_dir', type=str, default=None,
                               help="Specify SPAdes temporary directory using the SPAdes --tmp-dir "
                                    "option (default: make a temporary directory in the output "
@@ -912,10 +916,10 @@ def rotate_completed_replicons(graph, args, counter):
         log.log_section_header('Rotating completed replicons')
         log.log_explanation('Any completed circular contigs (i.e. single contigs which have one '
                             'link connecting end to start) can have their start position changed '
-                            'with altering the sequence. For consistency, Unicycler now searches '
-                            'for a starting gene (dnaA or repA) in each such contig, and if one '
-                            'is found, the contig is rotated to start with that gene on the '
-                            'forward strand.')
+                            'without altering the sequence. For consistency, Unicycler now '
+                            'searches for a starting gene (dnaA or repA) in each such contig, and '
+                            'if one is found, the contig is rotated to start with that gene on '
+                            'the forward strand.')
 
         rotation_result_table = [['Segment', 'Length', 'Depth', 'Starting gene', 'Position',
                                   'Strand', 'Identity', 'Coverage']]

unicycler/version.py

@@ -13,4 +13,4 @@ details. You should have received a copy of the GNU General Public License along
 not, see <http://www.gnu.org/licenses/>.
 """
 
-__version__ = '0.4.7'
+__version__ = '0.4.8'