Plots with poretools

[yk-tanigawa]

• generate plots with poretools
  • https://github.com/arq5x/poretools

[yk-tanigawa]

• basically, I would try all the functionality listed in this notebook with the data:
  • http://nbviewer.jupyter.org/github/arq5x/poretools/blob/master/poretools/ipynb/test_run_report.ipynb

[yk-tanigawa]

• poretools does not fully support the most recent file format
  • https://github.com/arq5x/poretools/issues/98

[yk-tanigawa]

• I also have a problem in installing rpy2 python package (this is only for visualization, but asking for help)

[yk-tanigawa]

• Decided to use Oxford Nanopore Tools

[yk-tanigawa]

analysis of the error

• Fast5File.py
• line 507
  • path = fastq_paths[self.version]['template'] % (self.group)
  • we encountered a key error about 'template'
• fastq_paths is a global variable in this program (lines 17-31), which handles the difference of data structure.

fastq_paths = {
  'closed' : {},
  'r9rnn' :         { 'template' : '/Analyses/Basecall_RNN_1D_%03d/BaseCalled_template'},
  'metrichor1.16' : { 'template' : '/Analyses/Basecall_1D_%03d/BaseCalled_template',
                      'complement' : '/Analyses/Basecall_1D_%03d/BaseCalled_complement',
                      'twodirections' : '/Analyses/Basecall_2D_%03d/BaseCalled_2D',
                      'pre_basecalled' : '/Analyses/EventDetection_000/Reads/'
                    },
  'classic' :       { 'template' : '/Analyses/Basecall_2D_%03d/BaseCalled_template',
                      'complement' : '/Analyses/Basecall_2D_%03d/BaseCalled_complement',
                      'twodirections' : '/Analyses/Basecall_2D_%03d/BaseCalled_2D',
                      'pre_basecalled' : '/Analyses/EventDetection_000/Reads/'
                    },
  'prebasecalled' : {'pre_basecalled' : '/Analyses/EventDetection_000/Reads/'}
}

• self.version is one of the followings and that is determined by self.guess_version() (line 218-)
  • r9nn. classic, metrichor1.16, prebasecalled

    def guess_version(self):
        """
        Try and guess the location of template/complement blocks
        """
        try:
            self.hdf5file["/Analyses/Basecall_RNN_1D_%03d/BaseCalled_template" % (self.group)]
            return 'r9rnn'
        except KeyError:
            pass

        try:
            self.hdf5file["/Analyses/Basecall_2D_%03d/BaseCalled_template" % (self.group)]
            return 'classic'
        except KeyError:
            pass

        try:
            self.hdf5file["/Analyses/Basecall_1D_%03d/BaseCalled_template" % (self.group)]
            return 'metrichor1.16'
        except KeyError:
            pass

        return 'prebasecalled'

• It's strange that the key 'template' is missing because self.version should be classic based on what we see in https://github.com/rivas-lab/nanopore/issues/8