latools/latools.py
def _minimal_export_traces(self, outdir=None, analytes=None,
                               samples=None, subset='All_Analyses'):
        """
        Used for exporting minimal dataset. DON'T USE.
        """
        if analytes is None:
            analytes = self.analytes
        elif isinstance(analytes, str):
            analytes = [analytes]

        if samples is not None:
            subset = self.make_subset(samples)

        samples = self._get_samples(subset)

        focus_stage = 'rawdata'
        # ud = 'counts'

        if not os.path.isdir(outdir):
            os.mkdir(outdir)

        for s in samples:
            d = self.data[s].data[focus_stage]
            out = Bunch()

            for a in analytes:
                out[a] = d[a]

            out = pd.DataFrame(out, index=self.data[s].Time)
            out.index.name = 'Time'

            d = dateutil.parser.parse(self.data[s].meta['date'])
            header = ['# Minimal Reproduction Dataset Exported from LATOOLS on %s' %
                      (time.strftime('%Y:%m:%d %H:%M:%S')),
                      "# Analysis described in '../analysis.lalog'",
                      '# Run latools.reproduce to import analysis.',
                      '#',
                      '# Sample: %s' % (s),
                      '# Analysis Time: ' + d.strftime('%Y-%m-%d %H:%M:%S')]

            header = '\n'.join(header) + '\n'

            csv = out.to_csv()

            with open('%s/%s.csv' % (outdir, s), 'w') as f:
                f.write(header)
                f.write(csv)
        return
def _minimal_export_traces(self, outdir=None, analytes=None,
                               samples=None, subset='All_Analyses'):
        if analytes is None:
            analytes = self.analytes
        elif isinstance(analytes, str):
            analytes = [analytes]

        if samples is not None:
            subset = self.make_subset(samples)

        samples = self._get_samples(subset)

        focus_stage = 'rawdata'
        # ud = 'counts'

        if not os.path.isdir(outdir):
            os.mkdir(outdir)

        for s in samples:
            d = self.data[s].data[focus_stage]
            out = Bunch()

            for a in analytes:
                out[a] = d[a]

            out = pd.DataFrame(out, index=self.data[s].Time)
            out.index.name = 'Time'

            d = dateutil.parser.parse(self.data[s].meta['date'])
            header = ['# Minimal Reproduction Dataset Exported from LATOOLS on %s' %
                      (time.strftime('%Y:%m:%d %H:%M:%S')),
                      "# Analysis described in '../analysis.lalog'",
                      '# Run latools.reproduce to import analysis.',
                      '#',
                      '# Sample: %s' % (s),
                      '# Analysis Time: ' + d.strftime('%Y-%m-%d %H:%M:%S')]

            header = '\n'.join(header) + '\n'

            csv = out.to_csv()

            with open('%s/%s.csv' % (outdir, s), 'w') as f:
                f.write(header)
                f.write(csv)
        return
def _minimal_export_traces ( self , outdir = None , analytes = None , samples = None , subset = 'All_Analyses' ) : if analytes is None : analytes = self . analytes elif isinstance ( analytes , str ) : analytes = [ analytes ] if samples is not None : subset = self . make_subset ( samples ) samples = self . _get_samples ( subset ) focus_stage = 'rawdata' # ud = 'counts' if not os . path . isdir ( outdir ) : os . mkdir ( outdir ) for s in samples : d = self . data [ s ] . data [ focus_stage ] out = Bunch ( ) for a in analytes : out [ a ] = d [ a ] out = pd . DataFrame ( out , index = self . data [ s ] . Time ) out . index . name = 'Time' d = dateutil . parser . parse ( self . data [ s ] . meta [ 'date' ] ) header = [ '# Minimal Reproduction Dataset Exported from LATOOLS on %s' % ( time . strftime ( '%Y:%m:%d %H:%M:%S' ) ) , "# Analysis described in '../analysis.lalog'" , '# Run latools.reproduce to import analysis.' , '#' , '# Sample: %s' % ( s ) , '# Analysis Time: ' + d . strftime ( '%Y-%m-%d %H:%M:%S' ) ] header = '\n' . join ( header ) + '\n' csv = out . to_csv ( ) with open ( '%s/%s.csv' % ( outdir , s ) , 'w' ) as f : f . write ( header ) f . write ( csv ) return
Used for exporting minimal dataset. DON'T USE.
Used for exporting minimal dataset . DON T USE .