Merge pull request #902 from deeptools/dev

Release 3.7.5

Author: lldelisle

docs/content/News.rst

@@ -1,6 +1,22 @@
 News and Developments
 =====================
 
+Release 3.7.5
+-------------
+**June 2024**
+
+- Update the version file.
+
+Release 3.7.4
+-------------
+**24 April 2024**
+
+- Allow chicAggregateStatistic.py to to extract the aggregated data from the views.hdf based on differential.hdf or differential_target.bed. Now the BED may have the target name in the 4th column. In that case, the aggregation is done per target.
+- Allow hicCorrectMatrix.py to write filtered out regions to a BED file
+
+Thanks @pavanvidem
+
+Warning: In this version the version file has not been modified so the tools gives 3.7.3 as version.
 
 Release 3.7.3
 -------------

hicexplorer/_version.py

@@ -2,4 +2,4 @@
 # This file is originally generated from Git information by running 'setup.py
 # version'. Distribution tarballs contain a pre-generated copy of this file.
 
-__version__ = '3.7.3'
+__version__ = '3.7.5'

hicexplorer/test/general/test_chicAggregateStatistic.py

@@ -33,6 +33,46 @@ def are_files_equal(file1, file2, delta=2, skip=0):
     return equal
 
 
+def test_target_list():
+    outfile_aggregate = NamedTemporaryFile(suffix='.hdf5', delete=False)
+    outfile_aggregate.close()
+    args = "--interactionFile {} --targetFile {} --outFileName {} \
+            -t {}".format(ROOT + 'chicViewpoint/two_matrices.hdf5',
+                          ROOT + 'chicAggregateStatistic/target_list_3col.bed',
+                          outfile_aggregate.name, 10).split()
+    chicAggregateStatistic.main(args)
+
+    aggregateFileH5Object = h5py.File(outfile_aggregate.name, 'r')
+    assert 'FL-E13-5_chr1_MB-E10-5_chr1' in aggregateFileH5Object
+    assert 'FL-E13-5_chr1' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']
+    assert 'MB-E10-5_chr1' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']
+
+    assert 'genes' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1']
+    assert 'genes' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1']
+    assert len(aggregateFileH5Object) == 1
+    assert aggregateFileH5Object.attrs['type'] == 'aggregate'
+
+    for chromosome in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1']:
+
+        assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'][chromosome]) == 3
+
+        for gene in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'][chromosome]:
+            assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'][chromosome][gene]) == 7
+            for data in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'][chromosome][gene]:
+                assert data in ['chromosome', 'end_list', 'gene_name', 'raw_target_list', 'relative_distance_list', 'start_list', 'sum_of_interactions']
+
+    for chromosome in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1']:
+
+        assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'][chromosome]) == 3
+
+        for gene in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'][chromosome]:
+            assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'][chromosome][gene]) == 7
+            for data in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'][chromosome][gene]:
+                assert data in ['chromosome', 'end_list', 'gene_name', 'raw_target_list', 'relative_distance_list', 'start_list', 'sum_of_interactions']
+
+    aggregateFileH5Object.close()
+
+
 def test_regular_mode():
     outfile_aggregate = NamedTemporaryFile(suffix='.hdf5', delete=False)
     outfile_aggregate.close()