Support for mcool files with hic_matrix_square

[mxw010]

Welcome to the pyGenomeTracks GitHub repository! Before opening the issue please check
that the following requirements are met :

• [ x ] Search whether this issue (or a similar issue) has been solved before
  using the search tab above. Link the previous issue if appropriate below.

• [ x ] Paste your pyGenomeTracks version (pyGenomeTracks --version) and your python
  version (python --version) below.

pyGenomeTracks --version
pyGenomeTracks 3.7

python --version
Python 3.9.12

Pretty sure this is due to the lack of support for .mcool file for some reason, because when I have

[hic matrix]
file = path-to-mcool.mcool::/resolutions/50000

in the .ini file I get

Traceback (most recent call last):
  File "~/.conda/envs/hicexplorer/lib/python3.9/site-packages/pygenometracks/tracksClass.py", line 677, in check_file_exists
    open(file_name_to_check, 'r').close()
FileNotFoundError: [Errno 2] No such file or directory: '~/path-to-file.mcool::/resolutions/50000'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "~/.conda/envs/hicexplorer/lib/python3.9/site-packages/pygenometracks/tracksClass.py", line 685, in check_file_exists
    open(name_with_tracks_path_to_check, 'r').close()
FileNotFoundError: [Errno 2] No such file or directory: '/~/path-to-file.mcool::/resolutions/50000'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "~/.conda/envs/hicexplorer/bin/pyGenomeTracks", line 11, in <module>
    main(args)
  File "~/.conda/envs/hicexplorer/lib/python3.9/site-packages/pygenometracks/plotTracks.py", line 274, in main
    trp = PlotTracks(args.tracks.name, args.width, fig_height=args.height,
  File "~/.conda/envs/hicexplorer/lib/python3.9/site-packages/pygenometracks/tracksClass.py", line 80, in __init__
    self.parse_tracks(tracks_file, plot_regions=plot_regions)
  File "~/.conda/envs/hicexplorer/lib/python3.9/site-packages/pygenometracks/tracksClass.py", line 604, in parse_tracks
    track_options = self.check_file_exists(track_options,
  File "~/.conda/envs/hicexplorer/lib/python3.9/site-packages/pygenometracks/tracksClass.py", line 688, in check_file_exists
    raise InputError(f"File in section [{track_dict['section_name']}] "
pygenometracks.utilities.InputError: File in section [3. [hic matrix]] not found:
~/path-to-file.mcool::/resolutions/50000

If I just feed the path to mcool, of course cooler complains that I didn't specify a group.

but when i change the file path to a .cool file, it plots nicely. hic_matrix already supports .mcool file so I would assume the code is already in place somewhere.

[lldelisle]

Hi,
I am sorry. When I implemented the squared matrix I forgot to change this line:

pyGenomeTracks/pygenometracks/tracksClass.py

Line 606 in c42e74e

track_options['file_type'] == 'hic_matrix')

I'll make a PR which corrects it later today.

[mxw010]

Thanks! I Appreciate the quick response.

[lldelisle]

I nearly forgot you. The PR is ready. I need to check with my colleagues if we do a quick bug fix release.

[TincaSubic]

Hi,

I came here from the documentation on 3.8 release.
I have pyGenomeTracks 3.8 and Python 3.8.16 and I am encountering the same issue as already mentioned in this thread. If I specify the group, I get an error that the file cannot be found. On the other hand if I do not specify a group, I get an error from cooler that I did not specify a group.

[lldelisle]

Hi,
This is really strange because we have a test for this:

pyGenomeTracks/pygenometracks/tests/test_hiCMatrixSquareTracks.py

Lines 289 to 305 in b8918d4

	def test_plot_tracks_with_mcool():
	outfile = NamedTemporaryFile(suffix='.png', prefix='pyGenomeTracks_test_',
	delete=False)
	args = "--tracks {0} --region X:2500000-3500000 "\
	"--trackLabelFraction 0.23 --width 38 " \
	"--dpi 130 --outFileName {1}" \
	"".format(os.path.join(ROOT,
	'mcool_hic_matrix_square.ini'),
	outfile.name).split()
	pygenometracks.plotTracks.main(args)
	res = compare_images(os.path.join(ROOT,
	'master_mcool_hic_matrix_square.png'),
	outfile.name, tolerance)
	assert res is None, res
	os.remove(outfile.name)

The ini file is here:

pyGenomeTracks/pygenometracks/tests/test_hiCMatrixSquareTracks.py

Lines 137 to 162 in b8918d4

	browser_tracks_with_mcool = """
	[x-axis]
	[mcool1]
	file = matrix.mcool::/0
	depth = 1000000
	file_type = hic_matrix_square
	[mcool2]
	file = matrix.mcool::/1
	depth = 1000000
	file_type = hic_matrix_square
	[mcool3]
	file = matrix.mcool::/2
	depth = 1000000
	file_type = hic_matrix_square
	[mcool4]
	file = matrix.mcool::/4
	depth = 1000000
	file_type = hic_matrix_square
	"""
	with open(os.path.join(ROOT, "mcool_hic_matrix_square.ini"), 'w') as fh:
	fh.write(browser_tracks_with_mcool)

And it passes.
Could you try to repeat this on your mcool file to be sure the way you specify the resolution is the good one?

$ cooler info matrix.mcool
Traceback (most recent call last):
  File "/home/ldelisle/.conda/envs/lastVersion/bin/cooler", line 10, in <module>
    sys.exit(cli())
  File "/home/ldelisle/.conda/envs/lastVersion/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/ldelisle/.conda/envs/lastVersion/lib/python3.9/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/ldelisle/.conda/envs/lastVersion/lib/python3.9/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/ldelisle/.conda/envs/lastVersion/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/ldelisle/.conda/envs/lastVersion/lib/python3.9/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/home/ldelisle/.conda/envs/lastVersion/lib/python3.9/site-packages/cooler/cli/_util.py", line 203, in decorated
    func(*args, **kwargs)
  File "/home/ldelisle/.conda/envs/lastVersion/lib/python3.9/site-packages/cooler/cli/info.py", line 41, in info
    c = Cooler(cool_uri)
  File "/home/ldelisle/.conda/envs/lastVersion/lib/python3.9/site-packages/cooler/api.py", line 85, in __init__
    self._refresh()
  File "/home/ldelisle/.conda/envs/lastVersion/lib/python3.9/site-packages/cooler/api.py", line 106, in _refresh
    raise KeyError(err_msg) from None
KeyError: "No cooler found at: matrix.mcool. Coolers found in ['/0', '/1', '/2', '/3', '/4']. Use '::' to specify a group path"
$ cooler info matrix.mcool::/0
{
    "bin-size": 640000,
    "bin-type": "fixed",
    "creation-date": "2018-02-14T15:11:28.401416",
    "format": "HDF5::Cooler",
    "format-url": "https://github.com/mirnylab/cooler",
    "format-version": 2,
    "generated-by": "cooler-0.7.6",
    "genome-assembly": "unknown",
    "nbins": 209,
    "nchroms": 5,
    "nnz": 21798,
    "sum": 2329145
}

[TincaSubic]

Thanks for a fast reply! The issue was pretty simple - I relied on building a .ini file using make_tracks_file. If I construct the ini file manually and use the above test with my mcool files, then everything works fine. Thanks!

…

On Thu, Jun 22, 2023 at 4:20 PM Lucille Delisle ***@***.***> wrote: Reopened #404 <#404>. — Reply to this email directly, view it on GitHub <#404 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A7PF5F43GBHJ3HR57SSOR7LXMSSHVANCNFSM5263TG3Q> . You are receiving this because you commented.Message ID: ***@***.***>