phageghost / python-genome-browser Goto Github PK

Hi, Should it be a commentary ?

File "/Users/lxf453/miniconda2/lib/python2.7/site-packages/pygbrowse/datasources.py", line 53
result: pandas.Series = self._query(query_chrom=query_chrom, query_start=query_start, query_end=query_end)
^
SyntaxError: invalid syntax

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)
in
----> 1 fig = genes_and_rna_plotter.visualize('4', 62494071, 62546083)

~/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.

File "C:\Users\User\AppData\Local\Programs\Python\Python311\Lib\subprocess.py", line 1509, in _execute_child
hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [WinError 2] The system cannot find the file specified

works on wsl but not on pycharm\windows