Adds unit-tests for dnatracing methods #593
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Also removes unused functions from dnatracing
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| plt.plot(coordinates_array[:, 0], coordinates_array[:, 1], "ko") | ||
| plt.savefig(f"{savename}_{dna_num}_coordinates.png") | ||
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Hi @ns-rse , would it be worth keeping writeCoordinates? I think it's fine to remove writeContourLengths given that we already have contour lengths in the all_statistics.csv spreadsheet, but do we have the coordinates printed out anywhere else? If not, it might be worth keeping it and producing it alongside other future tracing outputs when toggled on?
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I removed it as its not used anywhere in the code as far as I can tell.
If writing co-ordinates is something that is required it should be a function within the topostats.io module which handles input/output and imported where required.
As it stands this method also does two things...
- Writes a CSV file.
- Produces plots.
The later should be separated and may already be covered by functionality that already exists.
I've added the desire to write co-ordinates to CSV to #183 (see comment) since this isn't used and I would write it differently anyway to fit within the directory structure of output, use pathlib rather than os and so forth.
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While it's not used in the main branch, I do use it in my branch. When I merged some of my work into the main back when we were on TopoStats 1.0, I did not enable it as some of my work wasn't complete, but I did intend to keep it. The idea of this method is to produce the coordinates of the traces, so that when other tracing based measurements went wrong, I could always look at the csv files and the plots to check whether the tracing was satisfatory, so as long as the functionalities are covered elsewhere, deleting them here should be fine.
Codecov ReportPatch coverage:
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## main #593 +/- ##
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+ Coverage 80.84% 81.65% +0.81%
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Files 19 19
Lines 2814 2824 +10
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+ Hits 2275 2306 +31
+ Misses 539 518 -21
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Also removes unused functions from dnatracing
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