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CarragherLab / cptools2

Running cellprofiler on eddie3 / SGE clusters
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Job.create_commands fails when job is not chunked #1

Open Swarchal opened 7 years ago

Swarchal commented 7 years ago

Both python 2.7.12 and 3.5

For some reason the list of dataframes is becoming a list of strings.

Might be due to the weird list un-nesting going on.

AttributeError                            Traceback (most recent call last)
<ipython-input-4-f4074253aec3> in <module>()
----> 1 job.create_commands("pipeline.cppipe", "/home/scott/cptools_test_dir", "/home/scott/cptools_test_dir")

/home/scott/.local/lib/python2.7/site-packages/cptools2-0.1-py2.7.egg/cptools2/job.pyc in create_commands(self, pipeline, location, commands_location)
    167                 # write loaddata csv to disk
    168                 utils.write_loaddata(name=name, location=location,
--> 169                                      dataframe=dataframe)
    170                 # write filelist to disk
    171                 utils.write_filelist(img_list=img_list,

/home/scott/.local/lib/python2.7/site-packages/cptools2-0.1-py2.7.egg/cptools2/utils.pyc in write_loaddata(name, location, dataframe)
     25 def write_loaddata(name, location, dataframe):
     26     loaddata_name = os.path.join(location, "loaddata", name + ".csv")
---> 27     dataframe.to_csv(loaddata_name, index=False)
     28 
     29 

AttributeError: 'str' object has no attribute 'to_csv'