make verbose work

plasmidtron/PlasmidTron.py

@@ -28,6 +28,10 @@ def __init__(self,options):
 		self.min_contig_len             = options.min_contig_len
 		self.action                     = options.action
 		self.min_spades_contig_coverage = options.min_spades_contig_coverage
+
+
+		if self.verbose:
+			self.logger.setLevel(10)
 
 	def run(self):
 		os.makedirs(self.output_directory)

plasmidtron/SpadesAssembly.py

@@ -43,7 +43,7 @@ def sequence_coverage(self, contig_name):
 		#NODE_447_length_1644_cov_25.5669
 		m = re.search('cov_([\d]+)', contig_name)
 		if m and m.group(0):
-			return m.group(1)
+			return int(m.group(1))
 		else:
 			# return a number big enough that it will always keep the contig
 			return self.min_spades_contig_coverage + 1

run_tests.sh

@@ -1 +1,2 @@
+echo "Tests should not be run pathpipe-farm3" 
 python3 -m unittest discover -s plasmidtron/tests/ -p '*_test.py'

scripts/plasmidtron

@@ -21,15 +21,15 @@ parser = argparse.ArgumentParser(
 parser.add_argument('output_directory', help='Output directory', type=InputTypes.is_output_directory_valid )
 parser.add_argument('file_of_trait_fastqs', help='File of filenames of trait (case) FASTQs', type=InputTypes.is_file_of_trait_fastqs_valid)
 parser.add_argument('file_of_nontrait_fastqs', help='File of filenames of nontrait (control) FASTQs', type=InputTypes.is_file_of_nontrait_fastqs_valid)
-parser.add_argument('--action',	 '-a', help='Control how the traits kmers are filtered for assembly [%(default)s]', choices=['intersection','union'],  default = 'union')
-parser.add_argument('--kmer',	 '-k', help='Kmer to use, depends on read length [%(default)s]', type=InputTypes.is_kmer_valid,  default = 51)
-parser.add_argument('--min_contig_len',	 '-l', help='Minimum contig length in final assembly [%(default)s]', type=InputTypes.is_min_contig_len_valid, default = 3000)
-parser.add_argument('--min_spades_contig_coverage',	 '-s', help='Filter out contigs with low coverage. Set to 0 to keep all. [%(default)s]', type=InputTypes.is_min_spades_contig_coverage_valid, default = 25)
-parser.add_argument('--min_kmers_threshold',	 '-m', help='Exclude k-mers occurring less than this [%(default)s]', type=InputTypes.is_min_kmers_threshold_valid,  default = 25)
-parser.add_argument('--max_kmers_threshold',	 '-x', help='Exclude k-mers occurring more than this [%(default)s]', type=InputTypes.is_max_kmers_threshold_valid,  default = 254)
-parser.add_argument('--threads',  '-t', help='Number of threads [%(default)s]', type=InputTypes.is_threads_valid,  default = 1)
-parser.add_argument('--spades_exec',	 '-s', help='Set the SPAdes executable [%(default)s]', type=str,  default = 'spades.py')
-parser.add_argument('--verbose',  '-v', action='count', help='Turn on debugging [%(default)s]', default = 0)
+parser.add_argument('--action',	                     '-a', help='Control how the traits kmers are filtered for assembly [%(default)s]', choices=['intersection','union'],  default = 'union')
+parser.add_argument('--kmer',	                     '-k', help='Kmer to use, depends on read length [%(default)s]', type=InputTypes.is_kmer_valid,  default = 51)
+parser.add_argument('--min_contig_len',	             '-l', help='Minimum contig length in final assembly [%(default)s]', type=InputTypes.is_min_contig_len_valid, default = 3000)
+parser.add_argument('--min_spades_contig_coverage',	 '-c', help='Filter out contigs with low coverage. Set to 0 to keep all. [%(default)s]', type=InputTypes.is_min_spades_contig_coverage_valid, default = 25)
+parser.add_argument('--min_kmers_threshold',	     '-m', help='Exclude k-mers occurring less than this [%(default)s]', type=InputTypes.is_min_kmers_threshold_valid,  default = 25)
+parser.add_argument('--max_kmers_threshold',	     '-x', help='Exclude k-mers occurring more than this [%(default)s]', type=InputTypes.is_max_kmers_threshold_valid,  default = 254)
+parser.add_argument('--threads',                     '-t', help='Number of threads [%(default)s]', type=InputTypes.is_threads_valid,  default = 1)
+parser.add_argument('--spades_exec',	             '-s', help='Set the SPAdes executable [%(default)s]', type=str,  default = 'spades.py')
+parser.add_argument('--verbose',                     '-v', action='count', help='Turn on debugging [%(default)s]', default = 0)
 parser.add_argument('--version', action='version', version=str(version))
 
 options = parser.parse_args()