Phenotypes caused by reduced gene function are widely used to elucidate gene function and image-based RNA interference (RNAi) screens are routinely used to find and characterize genes involved in a particular biological process. In DNA staining of cells, nucleoli can be identified as the absence of DNA in nuclei ( Fig.
#Assertionerror cellprofiler threeshold mac os x
Any ideas? (I'm using Python 2.7.6 on Mac OS X 10.10.2 if that's helpful).The nucleolus is a prominent structure of the nucleus of eukaryotic cells and is involved in ribosome biogenesis and cell cycle regulation. 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='') Uni = parser.add_argument_group('universal optional arguments') 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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