doc updates and fixes

assemble/skani.py

@@ -82,14 +82,14 @@ def execute(self, subcommand, args, outfile, threads=None):
     def triangle(self, ref_fastas, outfile_ani, outfile_af, other_args = (), threads=None):
         ''' skani triangle computes an all-to-all ANI distance matrix for a set of sequences
         '''
-        self.execute('triangle', ref_fastas + other_args, outfile_ani, threads=threads)
+        self.execute('triangle', list(ref_fastas) + list(other_args), outfile_ani, threads=threads)
         shutil.copyfile('skani_matrix.af', outfile_af)
 
     def dist(self, query_fasta, ref_fastas, outfile, other_args = (), threads=None):
         ''' skani dist computes ANI distance between a specified query set of
             sequences (MAGs) and reference genomes (database)
         '''
-        self.execute('dist', ['-q', query_fasta, '-r'] + ref_fastas + other_args, outfile, threads=threads)
+        self.execute('dist', ['-q', query_fasta, '-r'] + list(ref_fastas) + list(other_args), outfile, threads=threads)
 
     def find_reference_clusters(self, ref_fastas,
                                 other_args = ('-m', 50, '--no-learned-ani', '--slow', '--robust', '--detailed', '--ci', '--sparse'),

assembly.py

@@ -428,9 +428,9 @@ def skani_contigs_to_refs(inContigs, inRefs, out_skani_dist, out_skani_dist_filt
 def parser_skani_contigs_to_refs(parser=argparse.ArgumentParser(description='Find closest references for contigs')):
     parser.add_argument('inContigs', help='FASTA file containing contigs')
     parser.add_argument('inRefs', nargs='+', help='FASTA files containing reference genomes')
-    parser.add_argument('out_skani_dist', help='Output file containing distances between contigs and references')
-    parser.add_argument('out_skani_dist_filtered', help='Output file containing distances between contigs and references, with only references that have a hit')
-    parser.add_argument('out_clusters_filtered', help='Output file containing clusters of highly-related genomes, with only references that have a hit')
+    parser.add_argument('out_skani_dist', help='Output file containing ANI distances between contigs and references')
+    parser.add_argument('out_skani_dist_filtered', help='Output file containing ANI distances between contigs and references, with only the top reference hit per cluster')
+    parser.add_argument('out_clusters_filtered', help='Output file containing clusters of highly-related genomes, with only clusters that have a hit to the contigs')
     util.cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))
     util.cmd.attach_main(parser, skani_contigs_to_refs, split_args=True)
     return parser