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obi ngsfilter: fixed a bug with -u option

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This commit is contained in:
Celine Mercier
2018-05-17 14:53:53 +02:00
parent 8a10072d99
commit a166a169cf
1 changed files with 4 additions and 2 deletions
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6
python/obitools3/commands/ngsfilter.pyx
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@ -353,20 +353,22 @@ def run(config):
info_view = info_input[1]
# Open the unidentified view
if config['ngsfilter']['unidentified'] is not None:
if 'unidentified' in config['ngsfilter'] and config['ngsfilter']['unidentified'] is not None: # TODO keyError if undefined problem
unidentified_input = open_uri(config['ngsfilter']['unidentified'],
input=False,
newviewtype=View_NUC_SEQS)
if unidentified_input is None:
raise Exception("Could not open the view containing the unidentified reads")
unidentified = unidentified_input[1]
else:
unidentified = None
# Initialize the progress bar
pb = ProgressBar(len(entries), config, seconde=5)
# Check and store primers and tags
infos = read_info_view(info_view, error=config['ngsfilter']['error'])
g = 0
u = 0
i = 0