Merge pull request #223 from rhysnewell/no-coassemble

assemble/recover: Require users to specify coassembly or not.

.gitignore

@@ -10,4 +10,5 @@ aviary_genome.egg-info
 
 example/
 test/data/.conda
+test/data/wgsim.metaspades.assembly.fna.fai
 config.yaml

aviary/aviary.py

@@ -792,13 +792,12 @@ def main():
     assemble_group.add_argument(
         '--coassemble', '--co-assemble', '--co_assemble',
         help='Specifies whether or not, when given multiple input reads, to coassemble them. \n'
-             'If False, Aviary will use the first set of short reads and first set of long reads to perform assembly \n'
+             'If False (no), Aviary will use the first set of short reads and first set of long reads to perform assembly \n'
              'All read files will still be used during the MAG recovery process for differential coverage.',
         type=str2bool,
         nargs='?',
         const=True,
-        dest='coassemble',
-        default=False,
+        metavar='yes|no',
     )
 
     assemble_group.add_argument(

aviary/modules/processor.py

@@ -233,7 +233,6 @@ def __init__(self,
             self.pe2 = 'none'
             self.short_percent_identity = 'none'
 
-
         try:
             self.kmer_sizes = args.kmer_sizes
             self.use_megahit = args.use_megahit
@@ -246,7 +245,7 @@ def __init__(self,
         except AttributeError:
             self.kmer_sizes = ['auto']
             self.use_megahit = False
-            self.coassemble = True
+            self.coassemble = False
             self.min_cov_long = 20
             self.min_cov_short = 3
             self.exclude_contig_cov = 100
@@ -346,6 +345,16 @@ def make_config(self):
 
         with open(template_conf_file) as template_config:
             conf = yaml.load(template_config)
+
+        if self.assembly == 'none' or self.assembly is None:
+            # Check if coassembly or not needs to be specified by the user.
+            if self.coassemble is None:
+                if (self.pe1 != 'none' and len(self.pe1) > 1) or \
+                   (self.longreads != 'none' and len(self.longreads) > 1):
+                    logging.error("Multiple readsets detected. Either specify '--coassemble' for coassembly of or '--coassemble no'.")
+                    sys.exit(-1)
+        if self.coassemble is None:
+            self.coassemble = False  # ensure that something is specified so that the config file is well formed
 
         if self.assembly != "none" and self.assembly is not None:
             self.assembly = list(dict.fromkeys([os.path.abspath(p) for p in self.assembly]))