mash fix

marbl · Jun 25, 2020 · d0725da · d0725da
1 parent 0aea58d
commit d0725da
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/parsnp b/parsnp
@@ -1015,7 +1015,7 @@ SETTINGS:
                             ref, 
                             "-l", all_genomes_fname],
                         stderr=open(os.path.join(outputDir, "mash.err"), 'w')).decode('utf-8')
-                    finalfiles = [line.split('\t')[0] for line in mash_out.split('\n')[1:] if line != '']
+                    finalfiles = [line.split('\t')[0] for line in mash_out.split('\n')[1:] if line != '' and len(line.split('\t')) > 1 and line.split('\t')[1].strip() != '']
                 elif use_ani:
                     if randomly_selected_ref:
                         subprocess.check_call([
@@ -1038,8 +1038,8 @@ SETTINGS:
                         for line in results:
                             # FastANI results file -> Query, Ref, ANI val, extra stuff,,,
                             line = line.split('\t')
-                            # if float(line[2]) >= min_ani_cutoff:
-                            genome_to_genomes[line[0]].add(line[1])
+                            if float(line[2]) >= min_ani_cutoff:
+                                genome_to_genomes[line[0]].add(line[1])
 
                         # for g in genome_to_genomes:
                             # print(len(g))