improve input check, add log

JaLuebke · Aug 29, 2022 · 1ec214a · 1ec214a
1 parent 8a5e232
commit 1ec214a
Showing 1 changed file with 22 additions and 11 deletions.
diff --git a/bakta/plot.py b/bakta/plot.py
@@ -71,22 +71,31 @@ def main():
  log.error('provided input annotation file not valid! path=%s', args.input)
  sys.exit(f'ERROR: input annotation file ({args.input}) not valid!')
  log.info('input-path=%s', annotation_path)
+ cfg.check_tmp_path(args)
 
  #Import Annotation Information
- input = open(args.input)
- annotation = json.load(input)
- input.close()
+ try:
+ with open(args.input, 'r') as input:
+ annotation = json.load(input)
+ except:
+ log.error('wrong file format!')
+ sys.exit('ERROR: wrong file format!')
  features = annotation['features']
  contigs = annotation['sequences']
 
  #Import Configuration Information
- with open(args.plot) as conf:
- config = yaml.load(conf, Loader=yaml.FullLoader)
- plots_string = config['plot']
- plots = plots_string.replace('-', '')
- plots = plots.replace("'", '')
- plots = plots.replace('"', '')
- plots = plots.split()
+ try:
+ with open(args.plot) as conf:
+ config = yaml.load(conf, Loader=yaml.FullLoader)
+ except:
+ log.error('wrong file format!')
+ sys.exit('ERROR: wrong file format!')
+
+ plots_string = config['plot']
+ plots = plots_string.replace('-', '')
+ plots = plots.replace("'", '')
+ plots = plots.replace('"', '')
+ plots = plots.split()
  plot_count = 1
  for p in plots:
  plot_contig = []
@@ -95,7 +104,7 @@ def main():
  plot_contig.append(c)
  break
 
-
+ print(f'drawing plot {plot_count}')
  write_plot(features,
  plot_contig,
  args.output,
@@ -108,6 +117,8 @@ def main():
  config['ngcs'])
  plot_count += 1
 
+ sys.exit('all plots are finished!')
+
 
 
 def write_plot(features,