From 8628b23d839f609315caa5a5a8fb0950b1a29b45 Mon Sep 17 00:00:00 2001 From: andrewjpage Date: Wed, 1 Feb 2017 13:28:38 +0000 Subject: [PATCH] make verbose work --- plasmidtron/PlasmidTron.py | 4 ++++ plasmidtron/SpadesAssembly.py | 2 +- ...varage.fa => expected_assembly_coverage.fa} | 0 run_tests.sh | 1 + scripts/plasmidtron | 18 +++++++++--------- 5 files changed, 15 insertions(+), 10 deletions(-) rename plasmidtron/tests/data/spadesassembly/{expected_assembly_covarage.fa => expected_assembly_coverage.fa} (100%) diff --git a/plasmidtron/PlasmidTron.py b/plasmidtron/PlasmidTron.py index 74688d0..97d9c5a 100755 --- a/plasmidtron/PlasmidTron.py +++ b/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) diff --git a/plasmidtron/SpadesAssembly.py b/plasmidtron/SpadesAssembly.py index f84f6d9..6b253ce 100644 --- a/plasmidtron/SpadesAssembly.py +++ b/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 diff --git a/plasmidtron/tests/data/spadesassembly/expected_assembly_covarage.fa b/plasmidtron/tests/data/spadesassembly/expected_assembly_coverage.fa similarity index 100% rename from plasmidtron/tests/data/spadesassembly/expected_assembly_covarage.fa rename to plasmidtron/tests/data/spadesassembly/expected_assembly_coverage.fa diff --git a/run_tests.sh b/run_tests.sh index b487801..5b67717 100755 --- a/run_tests.sh +++ b/run_tests.sh @@ -1 +1,2 @@ +echo "Tests should not be run pathpipe-farm3" python3 -m unittest discover -s plasmidtron/tests/ -p '*_test.py' diff --git a/scripts/plasmidtron b/scripts/plasmidtron index 5c39531..ae17fc5 100755 --- a/scripts/plasmidtron +++ b/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()