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Minor fixes

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This commit is contained in:
Celine Mercier
2018-08-10 10:39:46 +02:00
parent e096b929dc
commit 2dc7fcceac
2 changed files with 3 additions and 4 deletions
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2
python/obitools3/commands/head.pyx
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@ -63,7 +63,7 @@ def run(config):
# Create output view with the line selection # Create output view with the line selection
try: try:
o_view = selection.materialize(output_view_name, comments="obi head: "+str(config['head']['count'])+"\n") o_view = selection.materialize(output_view_name, comments="obi head: "+str(len(selection))+"\n")
except Exception, e: except Exception, e:
raise RollbackException("obi head error, rollbacking view: "+str(e), o_view) raise RollbackException("obi head error, rollbacking view: "+str(e), o_view)

5
python/obitools3/commands/sort.pyx
View File

@ -4,9 +4,8 @@ from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.dms import DMS from obitools3.dms import DMS
from obitools3.dms.view.view cimport View, Line_selection from obitools3.dms.view.view cimport View, Line_selection
from obitools3.uri.decode import open_uri from obitools3.uri.decode import open_uri
from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyInputOption, addMinimalOutputOption from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
from obitools3.dms.view import RollbackException from obitools3.dms.view import RollbackException
from functools import reduce
from obitools3.apps.config import logger from obitools3.apps.config import logger
from obitools3.dms.capi.obitypes cimport OBI_BOOL, \ from obitools3.dms.capi.obitypes cimport OBI_BOOL, \
OBI_CHAR, \ OBI_CHAR, \
@ -86,7 +85,7 @@ def run(config):
output_view_name = uri[0] output_view_name = uri[0]
# Initialize the progress bar # Initialize the progress bar
pb = ProgressBar(len(i_view), config, seconde=5) # TODO pb = ProgressBar(len(i_view), config, seconde=5)
keys = config['sort']['keys'] keys = config['sort']['keys']