![]() CellProfiler failed to remove the temporary file, /tmp/Cpmeasurementsi5feq24y.hdf5 and there it sits on your disk now. Any ideas? (I'm using Python 2.7.6 on Mac OS X 10.10.2 if that's helpful).File "/projects/verhaak-lab/amins/hpcenv/mambaforge/envs/cp2/lib/python3.8/site-packages/cellprofiler_core/utilities/hdf5_dict.py", line 435, in _getitem_Īssert feature_exists, "Feature does not exist".format(ĪssertionError: Feature ExportToDb_Images for Experiment does not exist I've tried removing all whitespace to no avail. I can't find a clear explanation for why this is happening. f, -suffix Suffix for multiplexed files h, -help show this help message and exit n, -noclean Do not delete intermediate files (for debuging) ![]() b, -bam Mapped read file type is bam (auto-detected if *.bam) The odd thing is that if I comment out ANY of the non-required arguments, I get the proper help text output, like this: usage: CountSNPLevelASE.py -m -s -r Self._print_message(self.format_help(), file)įile "/System/Library/Frameworks/amework/Versions/2.7/lib/python2.7/argparse.py", line 2301, in format_helpįile "/System/Library/Frameworks/amework/Versions/2.7/lib/python2.7/argparse.py", line 279, in format_helpįile "/System/Library/Frameworks/amework/Versions/2.7/lib/python2.7/argparse.py", line 209, in format_helpįile "/System/Library/Frameworks/amework/Versions/2.7/lib/python2.7/argparse.py", line 330, in _format_usage Start_index = consume_optional(start_index)įile "/System/Library/Frameworks/amework/Versions/2.7/lib/python2.7/argparse.py", line 1866, in consume_optionalįile "/System/Library/Frameworks/amework/Versions/2.7/lib/python2.7/argparse.py", line 1794, in take_actionĪction(self, namespace, argument_values, option_string)įile "/System/Library/Frameworks/amework/Versions/2.7/lib/python2.7/argparse.py", line 994, in _call_įile "/System/Library/Frameworks/amework/Versions/2.7/lib/python2.7/argparse.py", line 2327, in print_help Namespace, args = self._parse_known_args(args, namespace)įile "/System/Library/Frameworks/amework/Versions/2.7/lib/python2.7/argparse.py", line 1926, in _parse_known_args However, when I run this script, with the '-h' option, instead of printing the help text, it spits out the following error: Traceback (most recent call last):įile "/System/Library/Frameworks/amework/Versions/2.7/lib/python2.7/argparse.py", line 1688, in parse_argsĪrgs, argv = self.parse_known_args(args, namespace)įile "/System/Library/Frameworks/amework/Versions/2.7/lib/python2.7/argparse.py", line 1720, in parse_known_args ![]() Single.add_argument('-f','-suffix', action='store', dest='suff', help='Suffix for multiplexed files ', default='', metavar='') Single = parser.add_argument_group('single mode arguments') Mult.add_argument('-k','-mem', action='store', dest='memory', help='Memory for each job ', default='5000MB', metavar='') Mult.add_argument('-w','-walltime', action='store', dest='walltime', help='Walltime for each job ', default='3:00:00', metavar='') Mult.add_argument('-j','-jobs', action='store', dest='jobs', type=int, help='Divide into # of jobs ', default=100, metavar='') Mult = parser.add_argument_group('multi(plex) mode arguments') Uni.add_argument('-h', '-help', action='help', help='show this help message and exit') Uni.add_argument('-n','-noclean', action='store_true', dest='noclean', help='Do not delete intermediate files (for debuging)') Uni.add_argument('-t','-single', action='store_true', dest='single', help='Mapped reads are single-end ') Uni.add_argument('-b','-bam', action='store_true', dest='bam', help='Mapped read file type is bam (auto-detected if *.bam)') Uni.add_argument('-p','-prefix', action='store', dest='prefix', help='Prefix for temp files and output ', default='TEST', metavar='') Some major changes are as follows: We’ve redesigned the interface for selecting multiple image and object sets in measurement modules. We’ve listened to your feedback and made adjustments to the user interface with the goal of making the software easier to use. Uni = parser.add_argument_group('universal optional arguments') At its core, CellProfiler is built for scientists. Req.add_argument('-r','-reads', action='store', dest='reads', help='Mapped reads file ', required=True, metavar='') Req.add_argument('-s','-snps', action='store', dest='snps', help='SNP BED file', required=True, metavar='') Req.add_argument('-m','-mode', action='store', dest='mode', help='Operation mode', choices=, required=True, metavar='') Req = parser.add_argument_group('required arguments') Parser = argparse.ArgumentParser(description='Placeholder text', add_help=False) I'm trying to write a Python script with a lot of arguments that I'd like to break up into clear groups using the argparse module as follows: import argparse
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