For rna plotter -- TypeError: '<' not supported between instances of 'NoneType' and 'int'
I am trying to run the following part of the data from the demonstration:
genes_and_rna_plotter = pygbrowse.plots.GenomeBrowser([[rnaseq_plotter], [genemodel_plotter]]) fig = genes_and_rna_plotter.visualize('chr4', 62494071, 62546083)
I keep getting this error message, and I've tried troubleshooting but nothing seems to be working (the error is on the fig = genes_... line, the first line is able to run without error).
TypeError Traceback (most recent call last)
~/Desktop/gene-browser/env/lib/python3.7/site-packages/pygbrowse/plots.py in visualize(self, chrom, start, end, fig_width, row_heights, ax_spacing, num_xticks, seaborn_style) 758 for plot_object in plot_object_subset: 759 plot_object.plot(this_ax, chrom=chrom, ws=start, we=end, fig_width=fig_width, --> 760 row_height=row_heights[ax_idx]) 761 762 # ToDo: Refactor legend code to get colors and names from objects not from axes handles.
~/Desktop/gene-browser/env/lib/python3.7/site-packages/pygbrowse/plots.py in plot(self, ax, chrom, ws, we, fig_width, row_height) 372 vert_center = vert_span / 2 + ylim[0] 373 --> 374 this_plot_vector = self.data[chrom].loc[ws:we] 375 376 if self.convolution_kernel is not None:
~/Desktop/gene-browser/env/lib/python3.7/site-packages/pygbrowse/datasources.py in getitem(self, key) 37 query_end = key + 1 38 ---> 39 return self.parent_data_source.query(query_chrom=self.chrom, query_start=query_start, query_end=query_end) 40 41
~/Desktop/gene-browser/env/lib/python3.7/site-packages/pygbrowse/datasources.py in query(self, query_chrom, query_start, query_end) 58 59 def query(self, query_chrom, query_start, query_end): ---> 60 query_result = self._query(query_chrom=query_chrom, query_start=query_start, query_end=query_end) 61 62 if self.convolution_kernel is not None:
**~/Desktop/gene-browser/env/lib/python3.7/site-packages/pygbrowse/datasources.py in _query(self, query_chrom, query_start, query_end, read_handling) 115 done = False 116 with open(tag_filename, 'rt') as tag_file: --> 117 tag_file.seek(start_offset) 118 # print(start_offset) 119 while not done:
TypeError: '<' not supported between instances of 'NoneType' and 'int'**
Any help would be appreciated, I can't seem to get past this myself.