def main():
# Get command line options
opts, args = init_options()
print "Annotating " + opts.infile
all_replicons = common.read_replicon_names(opts.fasta)
# Separate multiple annotation files
annofile_list = opts.annofiles.split(",")
if len(annofile_list) != len(all_replicons):
print "ERROR: wrong number of replicon names for replicon files"
exit(1)
print "Using " + str(len(annofile_list)) + " .ptt files"
annotations = common.read_annotations(annofile_list, all_replicons)
lines_written = write_annotated(opts.infile, opts.outfile, annotations)
print str(lines_written) + " lines written to " + opts.outfile
def main():
# Get command line options
opts, args = init_options()
print "Annotating " + opts.infile
all_replicons = common.read_replicon_names(opts.fasta)
# Separate multiple annotation files
annofile_list = opts.annofiles.split(",")
if len(annofile_list) != len(all_replicons):
print "ERROR: wrong number of replicon names for replicon files"
exit(1)
print "Using " + str(len(annofile_list)) + " .ptt files"
annotations = common.read_annotations(annofile_list, all_replicons)
lines_written = write_annotated(opts.infile, opts.outfile, annotations)
print str(lines_written) + " lines written to " + opts.outfile
def main():
# Get command line options
opts, args = init_options()
print "Tabulating " + opts.infile
all_replicons = common.read_replicon_names(opts.fasta)
# Separate multiple annotation files
annofile_list = opts.annofiles.split(",")
if len(annofile_list) != len(all_replicons):
print "ERROR: wrong number of replicon names for replicon files"
exit(1)
print "Using annotation files " + str(annofile_list)
annotations = common.read_annotations(annofile_list, all_replicons)
(runs, hits, allhits) = read_hits_file(opts.infile)
lines_written = write_tabulated(opts.outfile, runs, annotations, hits, allhits)
def main():
# Get command line options
opts, args = init_options()
print "Tabulating " + opts.infile
all_replicons = common.read_replicon_names(opts.fasta)
# Separate multiple annotation files
annofile_list = opts.annofiles.split(",")
if len(annofile_list) != len(all_replicons):
print "ERROR: wrong number of replicon names for replicon files"
exit(1)
print "Using annotation files " + str(annofile_list)
annotations = common.read_annotations(annofile_list, all_replicons)
(runs, hits, allhits) = read_hits_file(opts.infile)
lines_written = write_tabulated(opts.outfile, runs, annotations, hits,
allhits)
module.__dict__['IMG_FOLDER'],
'benchmark.json')) as file:
benchmark_config = json.load(file)
classification = benchmark_config['classification']
classification_method = classification_map[classification]
encoding = benchmark_config['encoding']
types = benchmark_config['types']
parameters = benchmark_config['data']
## Load annotations
path = os.path.join('..', 'vision_images',
module.__dict__['IMG_FOLDER'])
annotations = common.read_annotations(path)
## Run benchmarks
output = pd.DataFrame(columns=[
'class', 'method', 'type', 'filename', 'found', 'missed', 'extra'
])
for b_name, benchmark in benchmarks.items():
b_instance = benchmark()
try:
b_instance.setup()
except AttributeError as e:
print(f"No setup method found for {b_name}.")
for m_name, method in benchmark.__dict__.items():