liniting

hicexplorer/__init__.py

@@ -1,7 +1,7 @@
 import logging
 logging.basicConfig(level=logging.DEBUG)
-import warnings 
+import warnings
 import sys
 
 if not sys.warnoptions:
-    warnings.simplefilter("ignore")
+    warnings.simplefilter("ignore")

hicexplorer/hicAggregateContacts.py

@@ -25,6 +25,7 @@
 warnings.simplefilter(action="ignore", category=RuntimeWarning)
 warnings.simplefilter(action="ignore", category=PendingDeprecationWarning)
 
+
 def parse_arguments(args=None):
     parser = argparse.ArgumentParser(add_help=False,
                                      description='Takes a list of positions in the hic-matrix and '

hicexplorer/hicAverageRegions.py

@@ -29,15 +29,15 @@ def parse_arguments(args=None):
     parserRequired.add_argument('--regions', '-r',
                                 help='BED file which stores a list of regions that are summed and averaged',
                                 required=True)
-    parserMutuallyExclusiveGroup = parser.add_mutually_exclusive_group(required=True)                 
+    parserMutuallyExclusiveGroup = parser.add_mutually_exclusive_group(required=True)
     parserMutuallyExclusiveGroup.add_argument('--range', '-ra',
-                                help='Range of region up- and downstream of each region to include in genomic units.',
-                                nargs=2,
-                                type=int)
+                                              help='Range of region up- and downstream of each region to include in genomic units.',
+                                              nargs=2,
+                                              type=int)
     parserMutuallyExclusiveGroup.add_argument('--rangeInBins', '-rib',
-                                help='Range of region up- and downstream of each region to include in bin units.',
-                                nargs=2,
-                                type=int)
+                                              help='Range of region up- and downstream of each region to include in bin units.',
+                                              nargs=2,
+                                              type=int)
     parserRequired.add_argument('--outFileName', '-out',
                                 help='File name to save the adjusted matrix.')
     parserOpt = parser.add_argument_group('Optional arguments')
@@ -55,7 +55,6 @@ def calculateViewpointRange(pHiCMatrix, pViewpoint, pRange):
     This function computes the correct start and end position of a viewpoint given the reference and the range.
     '''
 
-
     max_length = pHiCMatrix.getBinPos(pHiCMatrix.getChrBinRange(pViewpoint[0])[1] - 1)[2]
     bin_size = pHiCMatrix.getBinSize()
     _range = [pRange[0], pRange[1]]
@@ -71,11 +70,13 @@ def calculateViewpointRange(pHiCMatrix, pViewpoint, pRange):
         _range[1] = (max_length - int(pViewpoint[2])) + bin_size
     return region_start, region_end, _range
 
+
 def getBinIndices(pHiCMatrix, pViewpoint):
     return pHiCMatrix.getRegionBinRange(pViewpoint[0], pViewpoint[1], pViewpoint[2])
 
+
 def calculateViewpointRangeBins(pHiCMatrix, pViewpoint, pRange):
-    
+
     viewpoint_index = getBinIndices(pHiCMatrix, pViewpoint)[0]
     start = viewpoint_index - pRange[0]
     end = viewpoint_index + pRange[1]
@@ -125,5 +126,4 @@ def main(args=None):
 
     summed_matrix /= len(indices_values)
 
-
-    save_npz(args.outFileName, summed_matrix)
+    save_npz(args.outFileName, summed_matrix)

hicexplorer/hicBuildMatrix.py

@@ -36,7 +36,6 @@
 import logging
 log = logging.getLogger(__name__)
 
-import warnings
 warnings.simplefilter(action="ignore", category=RuntimeWarning)
 warnings.simplefilter(action="ignore", category=PendingDeprecationWarning)
 
@@ -1381,13 +1380,13 @@ def main(args=None):
     unlink(args.outFileName.name)
 
     if args.outFileName.name.endswith('.cool') and args.binSize is not None and len(args.binSize) > 2:
-        
+
         matrixFileHandlerOutput = MatrixFileHandler(pFileType='cool')
         matrixFileHandlerOutput.set_matrix_variables(hic_ma.matrix,
-                                                        hic_ma.cut_intervals,
-                                                        hic_ma.nan_bins,
-                                                        hic_ma.correction_factors,
-                                                        hic_ma.distance_counts)
+                                                     hic_ma.cut_intervals,
+                                                     hic_ma.nan_bins,
+                                                     hic_ma.correction_factors,
+                                                     hic_ma.distance_counts)
         matrixFileHandlerOutput.save(args.outFileName.name + '::/resolutions/' + str(args.binSize[0]), pSymmetric=True, pApplyCorrection=False)
 
         for resolution in args.binSize[1:]:

hicexplorer/hicConvertFormat.py

@@ -16,6 +16,7 @@
 
 from copy import deepcopy
 
+
 def parse_arguments(args=None):
     """
     get command line arguments
@@ -148,7 +149,7 @@ def main(args=None):
                 chromosomes_to_load = None
                 if args.chromosome:
                     chromosomes_to_load = [args.chromosome]
-                
+
                 applyCorrectionCoolerLoad = True
                 if args.load_raw_values:
                     applyCorrectionCoolerLoad = False
@@ -168,7 +169,6 @@ def main(args=None):
 
                 matrixFileHandlerOutput = MatrixFileHandler(pFileType=args.outputFormat, pEnforceInteger=args.enforce_integer, pFileWasH5=format_was_h5)
 
-
                 matrixFileHandlerOutput.set_matrix_variables(_matrix, cut_intervals, nan_bins,
                                                              correction_factors, distance_counts)
                 matrixFileHandlerOutput.save(
@@ -185,19 +185,18 @@ def main(args=None):
                     hic_matrix = HiCMatrix.hiCMatrix()
                     hic_matrix.setMatrix(_matrix, cut_intervals)
 
-
                     bin_size = hic_matrix.getBinSize()
 
                     for j, resolution in enumerate(args.resolutions):
                         hic_matrix_res = deepcopy(hic_matrix)
-                        
+
                         _mergeFactor = int(resolution) // bin_size
 
                         log.debug('bin size {}'.format(bin_size))
                         log.debug('_mergeFactor {}'.format(_mergeFactor))
                         if int(resolution) != bin_size:
                             merged_matrix = hicMergeMatrixBins.merge_bins(
-                            hic_matrix_res, _mergeFactor)
+                                hic_matrix_res, _mergeFactor)
                         else:
                             merged_matrix = hic_matrix_res
                         append = False

hicexplorer/hicMergeTADbins.py

@@ -39,7 +39,7 @@ def parse_arguments():
                         help='Name for the resulting matrix file.',
                         required=True)
     parser.add_argument('--version', action='version',
-                           version='%(prog)s {}'.format(__version__))
+                        version='%(prog)s {}'.format(__version__))
     return parser
 
 

hicexplorer/hicNormalize.py

@@ -104,4 +104,4 @@ def main(args=None):
             hic_matrix.matrix.data[mask] = 0
             hic_matrix.matrix.eliminate_zeros()
 
-            hic_matrix.save(args.outFileName[i], pApplyCorrection=False)
+            hic_matrix.save(args.outFileName[i], pApplyCorrection=False)

hicexplorer/hicPlotAverageRegions.py

@@ -14,8 +14,10 @@
 import matplotlib.cm as cm
 import matplotlib.gridspec as gridspec
 import numpy as np
-from  scipy.ndimage import  rotate
+from scipy.ndimage import rotate
 from mpl_toolkits.axes_grid1 import make_axes_locatable
+
+
 def parse_arguments(args=None):
 
     parser = argparse.ArgumentParser(
@@ -71,7 +73,7 @@ def parse_arguments(args=None):
 def main(args=None):
 
     args = parse_arguments().parse_args(args)
-    
+
     matrix = load_npz(args.matrix)
 
     matrix = matrix.toarray()
@@ -80,8 +82,8 @@ def main(args=None):
     matrix = rotate(matrix, 45)
     matrix_shapes = matrix.shape
     # log.debug('matrix.shapes {}'.format(matrix_shapes))
-    matrix = matrix[:matrix_shapes[0]//2, :]
-    norm=None
+    matrix = matrix[:matrix_shapes[0] // 2, :]
+    norm = None
     if args.vMax is not None or args.vMin is not None:
         matrix = matrix.clip(min=args.vMin, max=args.vMax)
     if args.log1p or args.log:
@@ -116,4 +118,4 @@ def main(args=None):
 
     fig.colorbar(matrix_axis, cax=cax)
     plt.tight_layout()
-    plt.savefig(args.outputFile, dpi=args.dpi)
+    plt.savefig(args.outputFile, dpi=args.dpi)

hicexplorer/hicPlotMatrix.py

@@ -34,6 +34,7 @@
 warnings.simplefilter(action="ignore", category=RuntimeWarning)
 warnings.simplefilter(action="ignore", category=PendingDeprecationWarning)
 
+
 def parse_arguments(args=None):
     parser = argparse.ArgumentParser(add_help=False,
                                      description='Creates a Heatmap of a HiC matrix.')

hicexplorer/hicTransform.py

@@ -39,7 +39,7 @@ def parse_arguments(args=None):
 
     parserOpt.add_argument('--method', '-me',
                            help='Transformation method to use for input matrix. Transformation is computed per chromosome.',
-                           choices=['obs_exp', 'obs_exp_lieberman', 'obs_exp_non_zero','pearson', 'covariance', 'norm'],
+                           choices=['obs_exp', 'obs_exp_lieberman', 'obs_exp_non_zero', 'pearson', 'covariance', 'norm'],
                            default='obs_exp')
 
     parserOpt.add_argument('--chromosomes',
@@ -86,20 +86,23 @@ def _obs_exp_norm(pSubmatrix):
     obs_exp_matrix_ = convertInfsToZeros(csr_matrix(obs_exp_matrix_)).todense()
     return obs_exp_matrix_
 
+
 def _obs_exp(pSubmatrix):
 
     obs_exp_matrix_ = obs_exp_matrix(pSubmatrix)
     obs_exp_matrix_ = convertNansToZeros(csr_matrix(obs_exp_matrix_))
     obs_exp_matrix_ = convertInfsToZeros(csr_matrix(obs_exp_matrix_)).todense()
     return obs_exp_matrix_
 
+
 def _obs_exp_non_zero(pSubmatrix):
 
     obs_exp_matrix_ = obs_exp_matrix_non_zero(pSubmatrix)
     obs_exp_matrix_ = convertNansToZeros(csr_matrix(obs_exp_matrix_))
     obs_exp_matrix_ = convertInfsToZeros(csr_matrix(obs_exp_matrix_)).todense()
     return obs_exp_matrix_
 
+
 def main(args=None):
 
     args = parse_arguments().parse_args(args)
@@ -114,7 +117,6 @@ def main(args=None):
     if args.chromosomes:
         hic_ma.keepOnlyTheseChr(args.chromosomes)
 
-
     trasf_matrix = lil_matrix(hic_ma.matrix.shape)
 
     if args.method == 'norm':
@@ -175,12 +177,11 @@ def main(args=None):
 
                 trasf_matrix[chr_range[0]:chr_range[1], chr_range[0]:chr_range[1]] = lil_matrix(_pearson(submatrix.todense()))
         else:
-            trasf_matrix= csr_matrix(_pearson(hic_ma.matrix.todense()))
-
+            trasf_matrix = csr_matrix(_pearson(hic_ma.matrix.todense()))
 
     elif args.method == 'covariance':
         if args.perChromosome:
-        
+
             for chrname in hic_ma.getChrNames():
                 chr_range = hic_ma.getChrBinRange(chrname)
                 submatrix = hic_ma.matrix[chr_range[0]:chr_range[1], chr_range[0]:chr_range[1]]

hicexplorer/test/general/test_hicAggregateContacts.py

@@ -90,7 +90,6 @@ def test_hicAggregateContacts_clustering():
     os.remove(outfile_heatmaps.name)
 
 
-
 @pytest.mark.skipif(MID_MEMORY > memory,
                     reason="Travis has too less memory to run it.")
 def test_hicAggregateContacts_clustering_cool():
@@ -140,7 +139,6 @@ def test_hicAggregateContacts_3d():
     os.remove(outfile_aggregate_3d.name)
 
 
-
 @pytest.mark.skipif(MID_MEMORY > memory,
                     reason="Travis has too less memory to run it.")
 def test_hicAggregateContacts_3d_cooler():

hicexplorer/test/general/test_hicAverageRegions.py

@@ -10,6 +10,7 @@
 
 ROOT = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "test_data/")
 
+
 def test_average_regions():
 
     outfile = NamedTemporaryFile(suffix='.npz', prefix='average_region', delete=False)
@@ -27,6 +28,7 @@ def test_average_regions():
 
     os.remove(outfile.name)
 
+
 def test_average_regions_range_in_bins():
 
     outfile = NamedTemporaryFile(suffix='.npz', prefix='average_region', delete=False)
@@ -40,4 +42,4 @@ def test_average_regions_range_in_bins():
 
     nt.assert_almost_equal(test_file.data, new_file.data, decimal=0)
 
-    os.remove(outfile.name)
+    os.remove(outfile.name)

hicexplorer/test/general/test_hicConvertFormat.py

@@ -54,13 +54,14 @@ def test_hicConvertFormat_h5_to_cool():
     nt.assert_array_almost_equal(test.matrix.data, new.matrix.data, decimal=DELTA_DECIMAL)
     # os.unlink(outfile.name)
 
+
 def test_hicConvertFormat_h5_to_cool_enforce_integer():
 
     # original_matrix = ''
     outfile = NamedTemporaryFile(suffix='.cool', delete=False)
     outfile.close()
 
-    args = "--matrices {} --outFileName {} --inputFormat h5 --outputFormat cool ".format(original_matrix_h5_li, outfile.name).split()
+    args = "--matrices {} --outFileName {} --inputFormat h5 --outputFormat cool ".format(original_matrix_cool, outfile.name).split()
     hicConvertFormat.main(args)
 
     test = hm.hiCMatrix(original_matrix_cool)
@@ -70,20 +71,21 @@ def test_hicConvertFormat_h5_to_cool_enforce_integer():
     print('issubclass(test.matrix.data.dtype.type, np.integer) {}'.format(issubclass(test.matrix.data.dtype.type, np.integer)))
     assert issubclass(test.matrix.data.dtype.type, np.integer)
 
+
 def test_hicConvertFormat_h5_to_homer():
     pass
     # os.unlink(outfile.name)
 
 
 def test_hicConvertFormat_h5_to_ginteractions():
     pass
-   
+
     # os.unlink(outfile.name)
 
 
 def test_hicConvertFormat_h5_to_mcool():
     pass
-   
+
     # os.unlink(outfile.name)
 
 

hicexplorer/test/general/test_hicFindTADs.py

@@ -74,30 +74,6 @@ def test_find_TADs_fdr_chromosomes():
 
     shutil.rmtree(tad_folder)
 
-# def test_find_TADs_fdr_dekker():
-#     # full test case with build of the matrix and search for tads
-#     matrix = ROOT + "dekker.txt.gz"
-#     tad_folder = mkdtemp(prefix="test_case_find_tads_fdr_dekker")
-#     args = "--matrix {} --minDepth 150000 --maxDepth 300000 --numberOfProcessors 2 --step 50000 \
-#     --outPrefix {}/test_multiFDR_dekker \
-#     --correctForMultipleTesting fdr".format(matrix, tad_folder).split()
-
-#     hicFindTADs.main(args)
-
-#     new = hm.hiCMatrix(tad_folder + "/test_multiFDR_dekker_zscore_matrix.h5")
-#     test = hm.hiCMatrix(ROOT + 'find_TADs/dekker/multiFDR_dekker_zscore_matrix.h5')
-#     nt.assert_equal(test.matrix.data, new.matrix.data)
-#     nt.assert_equal(test.cut_intervals, new.cut_intervals)
-
-#     print(tad_folder + "/test_multiFDR_boundaries.bed")
-#     assert are_files_equal(ROOT + "find_TADs/dekker/multiFDR_dekker_boundaries.bed", tad_folder + "/test_multiFDR_dekker_boundaries.bed")
-#     assert are_files_equal(ROOT + "find_TADs/dekker/multiFDR_dekker_domains.bed", tad_folder + "/test_multiFDR_dekker_domains.bed")
-#     assert are_files_equal(ROOT + "find_TADs/dekker/multiFDR_dekker_tad_score.bm", tad_folder + "/test_multiFDR_dekker_tad_score.bm")
-#     assert are_files_equal(ROOT + "find_TADs/dekker/multiFDR_dekker_boundaries.gff", tad_folder + "/test_multiFDR_dekker_boundaries.gff")
-#     assert are_files_equal(ROOT + "find_TADs/dekker/multiFDR_dekker_score.bedgraph", tad_folder + "/test_multiFDR_dekker_score.bedgraph")
-
-#     shutil.rmtree(tad_folder)
-
 
 def test_find_TADs_bonferroni():
     # reduced test case, the z-score matrix is given to decrease run time

hicexplorer/test/general/test_hicPCA.py

@@ -208,8 +208,6 @@ def test_pca_bigwig_gene_density_intermediate_matrices_norm():
 
     test_pearson_h5 = hm.hiCMatrix(ROOT + "hicPCA/pearson_norm.h5")
 
-
-
     nt.assert_array_almost_equal(test_pearson.matrix.data, new_pearson.matrix.data, decimal=DELTA_DECIMAL)
     nt.assert_array_almost_equal(test_obs_exp.matrix.data, new_obs_exp.matrix.data, decimal=DELTA_DECIMAL)