add new little requested features #875
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Added the following features:
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Tests need to be added |
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Please provide test cases and make sure it works with current python and numpy. Thanks! |
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I might have some test data but have to find some time. |
pavanvidem
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@joachimwolff @bgruening please review |
| for line in file.readlines(): | ||
| if line.startswith('#'): | ||
| continue | ||
| _line = line.strip().split('\t') |
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I find the variable name _line confusing. They are now elements or something like that.
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to be consistent with the remaining project I used _line. The same line of code can be found several times.
hicexplorer/hicCorrectMatrix.py
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| @@ -548,6 +551,7 @@ def filter_by_zscore(hic_ma, lower_threshold, upper_threshold, perchr=False): | |||
| to avoid introducing bias due to different chromosome numbers | |||
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| """ | |||
| print("filtering by z-score") | |||
hicexplorer/hicCorrectMatrix.py
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| @@ -658,9 +662,22 @@ def main(args=None): | |||
| restore_masked_bins=False) | |||
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| assert matrix_shape == ma.matrix.shape | |||
| for idx in outlier_regions: | |||
hicexplorer/hicCorrectMatrix.py
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| with open(args.filteredBed, 'w') as f: | ||
| for outlier_region in set(outlier_regions): | ||
| interval = ma.cut_intervals[outlier_region] | ||
| f.write('{}\t{}\t{}\t.\t{}\t.\n'.format(interval[0], |
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using an f-string here makes it much easier to read I suspect
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used a plain join because the interval should anyways contain 4 elements
hicexplorer/hicCorrectMatrix.py
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| # mask filtered regions | ||
| ma.maskBins(outlier_regions) | ||
| total_filtered_out = set(outlier_regions) | ||
| print(outlier_regions, "Bins that are MAD outliers ({:.2f}%) " |
| if x != y: | ||
| count = sum(1 for a, b in zip(x, y) if a != b) | ||
| if count > pDifference: | ||
| equal = False |
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you break here the entire loop, correct? than you can also return and remove the equal altogether
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I want to return true or false. Again copied this part from somewhere in the project.
| for line in file.readlines(): | ||
| if line.startswith('#'): | ||
| continue | ||
| _line = line.strip().split('\t') |
| try: | ||
| chrom, start, end = _line[:4] | ||
| except ValueError: | ||
| _line = line.strip().split() |
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When a line has less then 3 columns, this exception is raised, and then you are trying the same again?
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No, first split was with tabs. This one with white spaces, if the input BED file is not tab seperated.
| chrom, start, end = _line[:4] | ||
| except ValueError: | ||
| _line = line.strip().split() | ||
| chrom, start, end, gene = _line[:4] |
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This file should contain 4 columns.
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Maybe add a column, its really not clear that you are parsing here two different file-types.
requirements.txt
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| @@ -23,6 +23,6 @@ future >= 0.18 | |||
| tqdm >= 4.66 | |||
| hyperopt >= 0.2.7 | |||
| python-graphviz >= 0.20 | |||
| scikit-learn >= 1.3.1 | |||
| scikit-learn == 1.3.2 | |||
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this pin looks to strict to me, is >=1,3,2,<1.4 better?
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Currently, there is no other version between 1.3.2 and 1.4. I switched it to 1.3,1.4
setup.py
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| @@ -116,7 +116,7 @@ def checkProgramIsInstalled(self, program, args, where_to_download, | |||
| "tqdm >= 4.66", | |||
| "hyperopt >= 0.2.7", | |||
| "graphviz >= 0.20", | |||
| "scikit-learn >= 1.3.1", | |||
| "scikit-learn == 1.3.2", | |||
flake8 . --exclude=.venv,.build,planemo_test_env,build --ignore=E501,F403,E402,F999,F405,E712)py.test hicexplorer --doctest-modules)